[Blends-commit] r3436 - in /projects/med/tags: 1.3/ 1.3/config/ 1.3/debian/ 1.3/debian/oldchangelogs/ 1.3/menu/ 1.3/menu/bio-dev/ 1.3/menu/bio/ 1.3/menu/cms/ 1.3/menu/imaging-dev/ 1.3/menu/imaging/ 1.3/menu/physics/ 1.3/menu/practice/ 1.3/menu/tools/ 1.3/tasks/ 1.4/debian/ 1.5/debian/
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Sat Jun 23 12:46:47 UTC 2012
Author: tille
Date: Sat Jun 23 12:46:46 2012
New Revision: 3436
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3436
Log:
Add missing tag and missing control files which were not commited before
Added:
projects/med/tags/1.3/
projects/med/tags/1.3/AUTHORS
projects/med/tags/1.3/COPYING
projects/med/tags/1.3/Makefile (with props)
projects/med/tags/1.3/README
projects/med/tags/1.3/config/
projects/med/tags/1.3/config/conf
projects/med/tags/1.3/config/config (with props)
projects/med/tags/1.3/config/config.1
projects/med/tags/1.3/config/control
projects/med/tags/1.3/debian/
projects/med/tags/1.3/debian-med-tasks.desc
projects/med/tags/1.3/debian/changelog
projects/med/tags/1.3/debian/compat
projects/med/tags/1.3/debian/control
projects/med/tags/1.3/debian/control.stub
projects/med/tags/1.3/debian/copyright
projects/med/tags/1.3/debian/med-config.postinst.stub
projects/med/tags/1.3/debian/oldchangelogs/
projects/med/tags/1.3/debian/oldchangelogs/bio
projects/med/tags/1.3/debian/oldchangelogs/cms
projects/med/tags/1.3/debian/oldchangelogs/dent
projects/med/tags/1.3/debian/oldchangelogs/imaging
projects/med/tags/1.3/debian/oldchangelogs/imaging-dev
projects/med/tags/1.3/debian/oldchangelogs/tools
projects/med/tags/1.3/debian/rules (with props)
projects/med/tags/1.3/menu/
projects/med/tags/1.3/menu/bio/
projects/med/tags/1.3/menu/bio-dev/
projects/med/tags/1.3/menu/bio-dev/biomode.txt
projects/med/tags/1.3/menu/bio-dev/bioperl.txt
projects/med/tags/1.3/menu/bio-dev/libbio-ruby.txt
projects/med/tags/1.3/menu/bio-dev/libncbi6-dev.menu
projects/med/tags/1.3/menu/bio-dev/libvibrant6-dev.txt
projects/med/tags/1.3/menu/bio-dev/mcl.txt
projects/med/tags/1.3/menu/bio-dev/python-biopython.txt
projects/med/tags/1.3/menu/bio/blast2.menu
projects/med/tags/1.3/menu/bio/boxshade.txt
projects/med/tags/1.3/menu/bio/fastdnaml.html
projects/med/tags/1.3/menu/bio/fastlink.txt
projects/med/tags/1.3/menu/bio/gff2aplot.txt
projects/med/tags/1.3/menu/bio/gff2ps.txt
projects/med/tags/1.3/menu/bio/glimmer.txt
projects/med/tags/1.3/menu/bio/hmmer.txt
projects/med/tags/1.3/menu/bio/loki.txt
projects/med/tags/1.3/menu/bio/mipe.txt
projects/med/tags/1.3/menu/bio/molphy.txt
projects/med/tags/1.3/menu/bio/muscle.txt
projects/med/tags/1.3/menu/bio/ncbi-epcr.txt
projects/med/tags/1.3/menu/bio/ncbi-tools-bin.menu
projects/med/tags/1.3/menu/bio/ncbi-tools-x11.menu
projects/med/tags/1.3/menu/bio/phylip.txt
projects/med/tags/1.3/menu/bio/poa.txt
projects/med/tags/1.3/menu/bio/r-cran-qtl.txt
projects/med/tags/1.3/menu/bio/readseq.txt
projects/med/tags/1.3/menu/bio/sim4.txt
projects/med/tags/1.3/menu/bio/t-coffee.txt
projects/med/tags/1.3/menu/cms/
projects/med/tags/1.3/menu/cms/zope-zms.txt
projects/med/tags/1.3/menu/imaging/
projects/med/tags/1.3/menu/imaging-dev/
projects/med/tags/1.3/menu/imaging-dev/ctn-dev.txt
projects/med/tags/1.3/menu/imaging-dev/libgtkimreg-dev.txt
projects/med/tags/1.3/menu/imaging-dev/libmdc2-dev.txt
projects/med/tags/1.3/menu/imaging-dev/libminc0-dev.txt
projects/med/tags/1.3/menu/imaging/ctn.txt
projects/med/tags/1.3/menu/imaging/dcmtk.txt
projects/med/tags/1.3/menu/imaging/medcon.txt
projects/med/tags/1.3/menu/imaging/minc-tools.txt
projects/med/tags/1.3/menu/imaging/nifti-bin.txt
projects/med/tags/1.3/menu/physics/
projects/med/tags/1.3/menu/physics/octave.menu
projects/med/tags/1.3/menu/physics/r-base.menu
projects/med/tags/1.3/menu/practice/
projects/med/tags/1.3/menu/tools/
projects/med/tags/1.3/menu/tools/mencal.txt
projects/med/tags/1.3/tasks/
projects/med/tags/1.3/tasks.ctl
projects/med/tags/1.3/tasks/bio
projects/med/tags/1.3/tasks/bio-dev
projects/med/tags/1.3/tasks/cms
projects/med/tags/1.3/tasks/data
projects/med/tags/1.3/tasks/epi
projects/med/tags/1.3/tasks/his
projects/med/tags/1.3/tasks/imaging
projects/med/tags/1.3/tasks/imaging-dev
projects/med/tags/1.3/tasks/laboratory
projects/med/tags/1.3/tasks/pharmacy
projects/med/tags/1.3/tasks/physics
projects/med/tags/1.3/tasks/practice
projects/med/tags/1.3/tasks/psychology
projects/med/tags/1.3/tasks/statistics
projects/med/tags/1.3/tasks/tools
projects/med/tags/1.3/tasks/typesetting
projects/med/tags/1.4/debian/control
projects/med/tags/1.5/debian/control
Added: projects/med/tags/1.3/AUTHORS
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/AUTHORS?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/AUTHORS (added)
+++ projects/med/tags/1.3/AUTHORS Sat Jun 23 12:46:46 2012
@@ -1,0 +1,1 @@
+Andreas Tille <tille at debian.org>
Added: projects/med/tags/1.3/COPYING
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/COPYING?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/COPYING (added)
+++ projects/med/tags/1.3/COPYING Sat Jun 23 12:46:46 2012
@@ -1,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
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+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
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+If distribution of executable or object code is made by offering
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+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
Added: projects/med/tags/1.3/Makefile
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/Makefile?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/Makefile (added)
+++ projects/med/tags/1.3/Makefile Sat Jun 23 12:46:46 2012
@@ -1,0 +1,13 @@
+#!/usr/bin/make -f
+
+BLENDMAKEFILE=/usr/share/blends-dev/Makefile
+
+CheckBLENDMakefile := $(shell if [ -e $(BLENDMAKEFILE) ] ; then echo 1 ; else echo 0 ; fi)
+ifeq ($(CheckBLENDMakefile),1)
+ include $(BLENDMAKEFILE)
+else
+ err := $(shell echo "$(BLENDMAKEFILE) is missing. Please install blends-dev package!")
+endif
+
+dummy:
+ @echo $(err)
Propchange: projects/med/tags/1.3/Makefile
------------------------------------------------------------------------------
svn:executable = *
Added: projects/med/tags/1.3/README
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/README?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/README (added)
+++ projects/med/tags/1.3/README Sat Jun 23 12:46:46 2012
@@ -1,0 +1,10 @@
+This folder collects information on packages that have been built for
+the Debian Med Blend or that are currently prepared
+to be uploaded.
+
+If you want to add package descriptions, then edit the
+respective file in tasks/ and make sure to have read through
+http://blends.alioth.debian.org/blends/ch-sentinel.en.html.
+
+For more advanced issues please refer to the Blends paper in full and
+consider to talk back to Andreas Tille <tille at debian.org>.
Added: projects/med/tags/1.3/config/conf
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/config/conf?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/config/conf (added)
+++ projects/med/tags/1.3/config/conf Sat Jun 23 12:46:46 2012
@@ -1,0 +1,6 @@
+## This is a configuration file for Debian Med Blend
+## It is read after /etc/blends/blends.conf and can override or add variables
+
+## Some Blends do not build their name generic like "Debian #BLEND#" so
+## we need the correct name here
+BLENDNAME="Debian Med"
Added: projects/med/tags/1.3/config/config
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/config/config?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/config/config (added)
+++ projects/med/tags/1.3/config/config Sat Jun 23 12:46:46 2012
@@ -1,0 +1,6 @@
+#!/bin/sh
+## Prints some info about that package and lets auto-apt work
+dpkg --status `basename $0` | \
+ grep -v ^Priority | \
+ grep -v ^Section | \
+ grep -v ^Installed-Size
Propchange: projects/med/tags/1.3/config/config
------------------------------------------------------------------------------
svn:executable = *
Added: projects/med/tags/1.3/config/config.1
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/config/config.1?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/config/config.1 (added)
+++ projects/med/tags/1.3/config/config.1 Sat Jun 23 12:46:46 2012
@@ -1,0 +1,18 @@
+.TH med-config 1 "Oct 18, 2007" "Debian-Med"
+.SH NAME
+med-config \- general Debian-Med package information and auto-apt helper
+med-<meta_package_name> \- Debian-Med package information and auto-apt helper
+
+.SH SYNOPSIS
+.B med-config
+.B med-<meta_package_name>
+
+.SH DESCRIPTION
+Print just a simple information page about every med-* package
+of the Debian-Med Custom Debian Distribution. Each metapackage has a
+.I /usr/bin/med-<meta_package_name>
+file which should print some usefull informations and could be serve
+as auto-apt helper.
+
+.SH AUTHOR
+Andreas Tille <tille at debian.org>.
Added: projects/med/tags/1.3/config/control
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/config/control?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/config/control (added)
+++ projects/med/tags/1.3/config/control Sat Jun 23 12:46:46 2012
@@ -1,0 +1,33 @@
+Package: med-config
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.6)
+Conflicts: med-common
+Replaces: med-common
+Provides: med-common
+Description: Debian Med Project config package
+ This package provides the basic infrastructure of all med-* packages and is
+ needed by them.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med using debconf.
+ .
+ Other packages in Debian Med Project are:
+ .
+ * med-bio for biological research
+ * med-bio-dev for developing applications in biological research
+ * med-cms for publicating a medical site on the internet
+ * med-epi for epidemiology
+ * med-imaging for image processing
+ * med-imaging-dev for developing applications for image processing
+ * med-pharmacy for pharmaceutical research
+ * med-physics for radiation oncology, diagnostic imaging, related fields
+ * med-practice for general practitioners
+ * med-tools contains miscellaneous tools
+ * med-typesetting depends from useful tools for typesetting
+ .
+ Note: All these packages are so called metapackages. This means they are not
+ executable programs, but only links to other packages. This way you will
+ conveniently get all the non-commercial medical software which is available
+ for Debian GNU/Linux.
+
Added: projects/med/tags/1.3/debian-med-tasks.desc
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian-med-tasks.desc?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian-med-tasks.desc (added)
+++ projects/med/tags/1.3/debian-med-tasks.desc Sat Jun 23 12:46:46 2012
@@ -1,0 +1,288 @@
+Task: med-bio
+Section: debian-med
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+Relevance: 10
+Key:
+ med-bio
+Packages: list
+ altree
+ fastdnaml
+ njplot
+ tree-puzzle
+ treeviewx
+ fastlink
+ loki
+ r-cran-qtl
+ amap-align
+ blast2
+ boxshade
+ gff2aplot
+ hmmer
+ kalign
+ mafft
+ mummer
+ muscle
+ sim4
+ sibsim4
+ t-coffee
+ wise
+ exonerate
+ dialign
+ dialign-tx
+ poa
+ probcons
+ proda
+ seaview
+ sigma-align
+ emboss
+ embassy-domalign
+ embassy-domainatrix
+ last-align
+ maq
+ ssake
+ velvet
+ rnahybrid
+ adun.app
+ garlic
+ gamgi
+ gdpc
+ ghemical
+ gromacs
+ pymol
+ rasmol
+ r-other-bio3d
+ massxpert
+ plasmidomics
+ biosquid
+ gff2ps
+ ncbi-epcr
+ ncbi-tools-bin
+ ncbi-tools-x11
+ perlprimer
+ readseq
+ tigr-glimmer
+ melting
+ mipe
+ primer3
+ glam2
+ phyml
+ autodock
+ mustang
+ theseus
+
+Task: med-bio-dev
+Section: debian-med
+Description: Debian Med packages for development of micro-biology applications
+ This metapackage will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+Relevance: 10
+Key:
+ med-bio-dev
+Packages: list
+ bioperl
+ bioperl-run
+ libncbi6-dev
+ mcl
+ libvibrant6-dev
+ python-biopython
+ libbio-ruby
+ libbiojava-java
+ libqsearch-dev
+ libgenome-1.3-0-dev
+ libbio-mage-perl
+ libtfbs-perl
+ libgo-perl
+ r-cran-genetics
+ r-cran-haplo.stats
+ octave-bioinfo
+ libbio-graphics-perl
+ libbio-primerdesigner-perl
+ libace-perl
+
+Task: med-cms
+Section: debian-med
+Description: Debian Med content management systems
+ This metapackage will install packages which are useful to build a
+ content management system for medical care.
+Relevance: 10
+Key:
+ med-cms
+Packages: list
+
+Task: med-epi
+Section: debian-med
+Description: Debian Med epidemiology related packages
+ This metapackage will install tools that are useful in epidemiological
+ research. Several packages making use of the GNU R data language for
+ statistical investigation. It might be a good idea to read the paper
+ "A short introduction to R for Epidemiology" at
+ http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
+Relevance: 10
+Key:
+ med-epi
+Packages: list
+ epigrass
+ r-cran-epibasix
+ r-cran-epitools
+ r-cran-epi
+
+Task: med-imaging
+Section: debian-med
+Description: Debian Med imaging packages
+ This metapackage will install Debian packages which might be useful in
+ medical image processing.
+ .
+ It installs several packages supporting DICOM (Digital Imaging and
+ Communications in Medicine) which is the de-facto standard for medical
+ image management. The standard defines data structures and services for
+ the exchange of medical images and related information. The latest release
+ has been published in 2008 and consists of 18 parts.
+ .
+ For more information, you can visit the NEMA homepage
+ http://medical.nema.org/ .
+ .
+ The status of the official DICOM base standard plus all the
+ supplements and correction items are summarized at David Clunie's webpage:
+ http://www.dclunie.com/dicom-status/status.html
+ where you'll find direct links to the most recent yearly edition
+ ftp://medical.nema.org/medical/dicom/2008/ .
+Relevance: 10
+Key:
+ med-imaging
+Packages: list
+ amide
+ ctn
+ dicomnifti
+ imagej
+ minc-tools
+ medcon
+ python-nifti
+ xmedcon
+ dcmtk
+ nifti-bin
+ aeskulap
+ fslview
+ gwyddion
+ sofa-apps
+ python-mvpa
+ python-nipy
+
+Task: med-imaging-dev
+Section: debian-med
+Description: Debian Med packages for medical image development
+ This metapackage will install Debian packages which might be useful
+ for developing applications for medical image processing.
+Relevance: 10
+Key:
+ med-imaging-dev
+Packages: list
+ ctn-dev
+ cimg-dev
+ libminc-dev
+ libmdc2-dev
+ libnifti1-dev
+ libinsighttoolkit3-dev
+ libvolpack1-dev
+ python-mvpa
+ python-nipy
+
+Task: med-pharmacy
+Section: debian-med
+Description: Debian Med packages for pharmaceutical research
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+Relevance: 10
+Key:
+ med-pharmacy
+Packages: list
+ chemtool
+
+Task: med-physics
+Section: debian-med
+Description: Debian Med packages for medical physicists
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+Relevance: 10
+Key:
+ med-physics
+Packages: list
+ paw++
+ paw
+ octave3.0
+ r-base
+
+Task: med-practice
+Section: debian-med
+Description: Debian Med packages for practice management
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for practitioners to manage their practice.
+Relevance: 10
+Key:
+ med-practice
+Packages: list
+ gnumed-client
+ gnumed-server
+ libchipcard-tools
+ aeskulap
+
+Task: med-psychology
+Section: debian-med
+Description: Debian Med packages for psychology
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for psychological research.
+Relevance: 10
+Key:
+ med-psychology
+Packages: list
+ python-pyepl
+ praat
+ r-cran-foreign
+ r-cran-psy
+ psignifit
+ psychopy
+
+Task: med-statistics
+Section: debian-med
+Description: Debian Med statistics
+ This metapackage will install packages which are helpful to do statistics
+ with a special focus on tasks in medical care.
+Relevance: 10
+Key:
+ med-statistics
+Packages: list
+ r-cran-qvalue
+ r-cran-randomforest
+
+Task: med-tools
+Section: debian-med
+Description: Debian Med several tools
+ This metapackage will install tools for several purposes in health care.
+ Currently it contains some simple programs for Personal Health.
+Relevance: 10
+Key:
+ med-tools
+Packages: list
+ mencal
+ cycle
+ pondus
+ wgerman-medical
+ hunspell-de-med
+
+Task: med-typesetting
+Section: debian-med
+Description: Debian Med support for typesetting and publishing
+ This metapackage will install Debian packages that might be helpful
+ for typesetting and publishing in medical care and structural
+ biology.
+Relevance: 10
+Key:
+ med-typesetting
+Packages: list
+ texlive-science
+ texlive-latex-extra
+
Added: projects/med/tags/1.3/debian/changelog
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/changelog?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/changelog (added)
+++ projects/med/tags/1.3/debian/changelog Sat Jun 23 12:46:46 2012
@@ -1,0 +1,371 @@
+debian-med (1.3) unstable; urgency=low
+
+ * tasks/physics: Enhanced information about biosig
+ * tasks/*: Several changes and additional information for a
+ lot of prospective packages; a certain amount of packages
+ is now available as official packages
+ * debian/control.stub:
+ - Fixed Vcs-Svn (missing svn/)
+ * Replaced some remaining "cdd" strings in the docs by "blends"
+ * Standards-Version: 3.8.3 (no changes needed)
+ * config/control: Depends: blends-common (>= 0.6.6)
+ Closes: #542656
+
+ -- Andreas Tille <tille at debian.org> Fri, 21 Aug 2009 14:09:18 +0200
+
+debian-med (1.2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * Bumped policy to 3.8.1 and make use of the new feature that
+ debian/control allows comment lines starting with # with no
+ preceding whitespace. [Policy paragraph 5.2]
+ * debhelper (>=7)
+ * Added med-statistics
+ * tasks/bio: Replaced biococoa.app by sequenceconverter.app
+ * tasks/bio-dev: Added libbiococoa-dev
+ * Build-Depends: blends-dev (0.6.3) to make sure no useless
+ metapackages with no dependency available in Debian will be
+ created
+ * tasks.ctl: Added missing tasks; tasks data, his, laboratory
+ which do not yet feature an existing depenency in Debian
+ were set to priority-none.
+
+ [ Michael Hanke ]
+ * Added ODIN to imaging task.
+ * Added VIA to the imaging task.
+ * Updated LIPSIA item to ppoint to the packaging VCS and note ITP.
+
+ -- Andreas Tille <tille at debian.org> Mon, 30 Mar 2009 07:56:56 +0200
+
+debian-med (1.1) experimental; urgency=low
+
+ * Make use of blends-dev instead of cdd-dev
+ * Versioned build depends from blends-dev >= 0.6.1 because this
+ also supports dist experimental
+ * Adapted Vcs fields to new location (cdd -> blends)
+ * tasks/practice: Depends: aeskulap
+ * Added link to tasks page in long description of med-tasks
+ (thanks to James Busser <jbusser at interchange.ubc.ca> for the
+ hint)
+ * tasks/*: several updates of newly uploaded packages and
+ prospective packages
+
+ -- Andreas Tille <tille at debian.org> Tue, 06 Jan 2009 10:01:49 +0100
+
+debian-med (1.0) unstable; urgency=low
+
+ * tasks/bio-dev
+ - Added libgenome
+ - Added libmems as prospective package
+ - Moved bioconductor from bio to bio-dev
+ - Added prospective projects where Steffen Möller started some
+ packaging work
+ - libqsearch -> libqsearch-dev
+ * tasks/bio
+ - Added prospective projects where Steffen Möller started some
+ packaging work
+ - Suggests: texlive-latex-extra (because of TeXShade)
+ - Removed line breaks in Dependencies, because cdd-gen-control
+ is not compliant to RFC 822 and requires '\' at the end of
+ lines to continue parsing the tasks files. To simply circumvent
+ this problem the relevant lines were concatenated to not miss
+ the dependencies in the resulting control file
+ - Renamed dialign-t to dialign-tx
+ * tasks/tools
+ - Added mssstest
+ - Added wgerman-medical, hunspell-de-med (remark: these are not
+ really tools but we have no better section, typesetting might be
+ an option but does also fit not really good)
+ * tasks/imaging
+ - Added prospective packages from static page
+ * tasks/imaging-dev
+ - Removed libgtkimreg
+ - Added libvtk5
+ - Added prospective packages from static page
+ - libminc0-dev | libminc-dev -> libminc-dev
+ - insighttoolkit -> insighttoolkit3
+ * tasks/physics
+ - octave | octave2.1 -> octave3.0
+ * debian/control.stub: XS-DM-Upload-Allowed -> DM-Upload-Allowed
+ * Standards-Version: 3.8.0 (no changes needed)
+ * Fixed typing of Debian Med: sed -i 's/Debian-Med/Debian Med/' *
+
+ -- Andreas Tille <tille at debian.org> Mon, 30 Jun 2008 09:59:37 +0200
+
+debian-med (0.17) unstable; urgency=low
+
+ * tasks/bio:
+ - Added emboss-kaptain as prospective package
+ - Added agdbnet as prospective package
+ - Added autodock, exonerate
+ - Suggests biococoa.app: Only suggests because status is
+ questionable
+ - Removed bugsx which is not really biology related
+ - Added gamgi as prospective package
+ - Moved unoffical and prospective packages from static
+ web pages to tasks file
+ * tasks/bio-dev:
+ - Added aceperl as prospective package
+ - Added libgff-perl as prospective package
+ - Added Recommends: libqsearch
+ * tasks/imaging
+ - Removed paul
+ - pngquant: Recommends -> Suggests
+ - Added gdmc as prospective package
+ - Added dicom4j as prospective package
+ * tasks/epi: New meta package: med-epi for epidemiology
+ research
+ * tasks/tools:
+ - Moved NetEpi prospective package to epi where it really
+ belongs to
+ - Added pondus
+ * Removed remark about recommended and suggested packages
+ from description or meta packages
+ * Build-Depends-Indep: cdd-dev (>= 0.5.0) which ensures that the
+ source tarball is builded properly and no network access is neede
+ to build the package
+ Closes: #470271
+
+ -- Andreas Tille <tille at debian.org> Wed, 20 Feb 2008 13:31:25 +0100
+
+debian-med (0.16) unstable; urgency=low
+
+ * New upstream version
+ * Standards-Version: 3.7.3 (no changes needed)
+ * Added Vcs-Browser / Vcs-Svn tags
+ * tasks/imaging:
+ - Added Dr. Jekyll, libvista2 and dcm4che as prospective package
+ - Fixed minc and nifti library depends
+ - odin, gwyddion and many more as prospective package
+ - Removed libfslio1, libniftiio0 which are only available in Etch
+ - Suggests: Imview
+ * tasks/imaging-dev:
+ - libvista2-dev as prospective package
+ - Fixed minc-dev and nifti-dev library depends
+ - Removed libniftiio0-dev which is only available in Etch
+ * tasks/bio
+ - Added ballview and mustang as prospective packages
+ - dialign-t is now official package - removed long
+ description
+ - Added glam2 as prospective package
+ - textopo is now in texlilve-science, decreased this from Recommends
+ to Suggests to not spoil systems with whole texlive installation
+ * tasks/bio-dev: Added BioClipse as prospective package
+ Pkg-Description
+ * tasks/practice:
+ - Added Mirth as prospective package
+ - Fixed libchipcard depends
+ * Debian-Med packaging policy:
+ - Maintainer: Debian-Med Packaging Team
+ <debian-med-packaging at lists.alioth.debian.org>
+ - XS-DM-Upload-Allowed: yes
+ - Uploaders: Andreas Tille <tille at debian.org>
+ - Vcs-Browser, Vcs-Svn
+ * Increased mozilla-biofox from Suggests to Recommends. Installation of
+ firefox as Dependency of this package should be no real problem.
+ * Increased bugsx from Suggests to Recommends. It is automatically decreased
+ to Suggests by cdd-gen-control so there is no need to decrease it in the
+ tasks file.
+ * Make tasks files compliant with rfc822 to be able to use python-debian
+ tools successfully. That means basically to have exactly one
+ Depends/Recommends/Suggest per paragraph so the fix was to insert some
+ newlines and remove '\' in end of lines
+ * tasks/tools: Fixed description
+ * tasks/practice: tinyheb as prospective package
+ * Increased Build-Dep version cdd-dev (>= 0.4.7) because
+ 0.4.5 and 0.4.6 are broken
+ * config/control: med-config Depends cdd-common (>= 0.4.7)
+
+ -- Andreas Tille <tille at debian.org> Tue, 19 Feb 2008 17:07:36 +0100
+
+debian-med (0.15) unstable; urgency=low
+
+ * med-imaging-dev: Added
+ Depends: libinsighttoolkit-dev
+ Suggests: insighttoolkit-examples
+ * med-imaging(-dev): Depend from libniftiio1(-dev) instead of
+ libniftiio0(-dev)
+ Closes: #448903
+ * Increased Build-Dep version cdd-dev (>= 0.4.4)
+ * Standards-Version: 3.7.3 (no changes needed)
+ * Added several prospective packages in tasks
+
+ -- Andreas Tille <tille at debian.org> Sun, 07 Oct 2007 18:25:56 +0200
+
+debian-med (0.14) unstable; urgency=low
+
+ * Builded using new cdd-dev 0.4
+ - med-common is now renamed to med-config
+ - additional package med-tasks
+ * med-bio: added emboss
+ * med-imaging: amide, dicomnifti, imagej, python-nifti
+ decreased paul from Recommends to Suggests
+ * med-imaging-dev: cimg-dev
+ decreased libgtkimreg-dev from Recommends to Suggests
+ * med-practice: libchipcard3c1, libchipcard3d0
+
+ -- Andreas Tille <tille at debian.org> Sat, 11 Aug 2007 17:50:29 +0200
+
+debian-med (0.13) unstable; urgency=low
+
+ * Removed entry for gnumed-client-debug because this package does
+ not exist any more. Removed gnumed-client menu as well because
+ this should be builded automatically from menu entry inside
+ gnumed-client package
+ Closes: #429217
+ * Added several packages to med-bio and reordering the task to
+ specific fields
+ * Imaging: Added dicomnifti
+ * Enhanced long description of med-common
+ * Remove header from po.stub/de.po because cdd-dev will add another
+ one
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Jun 2007 16:23:36 +0200
+
+debian-med (0.12) unstable; urgency=low
+
+ * Changed med-practice menu
+ Closes: #385584
+ Use menu entry for gnumed-client-debug that regards #389932.
+ Note: gnumed-client-debug is not in the med-practice dependency
+ list but it is suggested by gnumed-client. So *if* the package
+ is installed at the box then an additional menu item occures correctly
+ in the Debian-Med menu. If it is not installed, only gnumed-client
+ is shown in the menu.
+ * med-bio: Added alternative to tree-puzzle as tree-ppuzzle
+ * Drop med-dent because odontolinux was removed from Debian
+ * med-bio: Added poa
+ Moved vrom Suggests to Depends: seaview (now really free)
+ Suggests: wise-doc
+ * med-imaging: Depends: libfslio0, libniftiio0, nifti-bin
+ Suggests:
+ * med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev
+ Suggests: libnifti-doc
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Sep 2006 15:28:51 +0200
+
+debian-med (0.11) unstable; urgency=low
+
+ * bugsx to from Depends to Suggets because this package moved to non-free
+ Closes: #383265
+ * Standards-Version: 3.7.2
+ Build-Depends: debhelper
+ * med-bio:
+ Depends: gromacs, dialign, kalign, probcons, wise, amap-align, biosquid
+ Suggests: mozilla-biofox
+ * debian/compat: 5
+ * Uploaders: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Aug 2006 10:07:41 +0200
+
+debian-med (0.10.1) unstable; urgency=low
+
+ * Make med-common depend from ${misc:Depends}
+ Closes: #331797
+ * Now med-practice really depends from gnumed-client which is now
+ awailable at Debian mirror
+
+ -- Andreas Tille <tille at debian.org> Wed, 5 Oct 2005 07:55:13 +0200
+
+debian-med (0.10) unstable; urgency=low
+
+ * Rebuilded with cdd-dev 0.3.11 (and increased versioned dependency
+ because 0.3.10 created broken *.dsc file)
+ Closes: #328428
+ * Standards-Version: 3.6.2 (no changes necessary)
+ * Added dependencies:
+ med-bio: mipe, sim4, perlprimer
+ med-bio-dev: libbio-ruby
+ * Addes meta package: med-practice
+
+ -- Andreas Tille <tille at debian.org> Sun, 25 Sep 2005 21:14:47 +0200
+
+debian-med (0.9) unstable; urgency=low
+
+ * Removed gnutrion from tools because it was removed from Debian at all
+ * Rebuilded with cdd-dev 0.3.10 version
+ * med-bio:
+ Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
+ Suggests: arb
+ * med-bio-dev
+ Recommends: libvibrant6-dev
+ Why: libmotif-dev conflicts lesstif-dev, so if someone wants to
+ install libmotif-dev it must be possible to deinstall
+ libvibrant6-dev without beeing forced to deinstall med-bio-dev
+ as well
+ Depends: python-biopython
+ * med-imaging:
+ paul now Recommends not Depends
+ Depends: dcmtk
+ Recommends: pngquant
+ * med-tools:
+ Depends: cycle
+ Suggests: cl-pubmed
+ Strong dependency would cost installing a large amount
+ of Common Lisp tools which in most cases is not worth
+ the effort
+ * Added user menu entries: bio/gff2aplot.txt, bio/gff2ps.txt,
+ bio/muscle.txt, bio/t-coffee.txt, bio/boxshade.txt,
+ bio-dev/python-biopython.txt, imaging/dcmtk.txt
+ * Added charset to debian/po.stub/de.po
+
+ -- Andreas Tille <tille at debian.org> Sun, 24 Oct 2004 20:59:03 +0200
+
+debian-med (0.8.9) experimental; urgency=low
+
+ * New upstream version which now uses the features of cdd-dev 0.3.9
+ * Exclude .svn dirs in dist target of debian/rules
+
+ -- Andreas Tille <tille at debian.org> Fri, 16 Jul 2004 11:33:21 +0200
+
+debian-med (0.8.3) unstable; urgency=high
+
+ * Rebuilded again against cdd-dev 0.3.4 which really closes the
+ mentioned bug.
+ * Urgency set to high because it *really* fixes a grave bug.
+
+ -- Andreas Tille <tille at debian.org> Thu, 15 Jul 2004 10:59:25 +0200
+
+debian-med (0.8.2) unstable; urgency=high
+
+ * Rebuilded with cdd-dev 0.3.3 which closes a grave bug (which
+ was reassigned to cdd-dev and thus it is not closed in this
+ changelog).
+ * Please make sure that all ${HOME}/.menu/cdd-menu files or
+ ${HOME}/.menu/med-* files are removed - they will not be
+ needed any more.
+
+ -- Andreas Tille <tille at debian.org> Wed, 14 Jul 2004 21:42:24 +0200
+
+debian-med (0.8.1) unstable; urgency=low
+
+ * Adjust versioned dependency of med-common from cdd-common
+ Closes: #258373
+
+ -- Andreas Tille <tille at debian.org> Fri, 9 Jul 2004 09:18:49 +0200
+
+debian-med (0.8) unstable; urgency=low
+
+ * Added med-physics, med-pharmacy, med-bio-dev
+ * Overworked menus of meta packages
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Jun 2004 14:44:36 +0200
+
+debian-med (0.7) unstable; urgency=low
+
+ * Switched to new version of cdd package (0.3) which has many
+ enhancements (no really important changes to the Debian-Med stuff
+ except that the packages have to be rebuilded with cdd-dev).
+ * New cdd-dev package cares for versioned dependency on med-common
+ Closes: #244903
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Apr 2004 11:21:16 +0200
+
+debian-med (0.6) unstable; urgency=medium
+
+ * Took over Debian-Edu method to build metapackages from one
+ common source.
+ The changelogs of the previous single meta package sources
+ can be found in the source package under debian/oldchangelogs.
+
+ -- Andreas Tille <tille at debian.org> Mon, 22 Mar 2004 19:21:55 +0100
Added: projects/med/tags/1.3/debian/compat
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/compat?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/compat (added)
+++ projects/med/tags/1.3/debian/compat Sat Jun 23 12:46:46 2012
@@ -1,0 +1,1 @@
+7
Added: projects/med/tags/1.3/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/control?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/control (added)
+++ projects/med/tags/1.3/debian/control Sat Jun 23 12:46:46 2012
@@ -1,0 +1,193 @@
+# This file is autogenerated via make -f debian/rules dist. Do not edit!
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7)
+Build-Depends-Indep: blends-dev (>= 0.6.6)
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
+
+Package: med-tasks
+Architecture: all
+Depends: tasksel
+Description: Debian Med tasks for tasksel
+ This package provides Debian Med tasks in tasksel.
+ .
+ These tasks are described in detail at
+ http://debian-med.alioth.debian.org/tasks/
+
+Package: med-config
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.6)
+Conflicts: med-common
+Replaces: med-common
+Provides: med-common
+Description: Debian Med Project config package
+ This package provides the basic infrastructure of all med-* packages and is
+ needed by them.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med using debconf.
+ .
+ Other packages in Debian Med Project are:
+ .
+ * med-bio for biological research
+ * med-bio-dev for developing applications in biological research
+ * med-cms for publicating a medical site on the internet
+ * med-epi for epidemiology
+ * med-imaging for image processing
+ * med-imaging-dev for developing applications for image processing
+ * med-pharmacy for pharmaceutical research
+ * med-physics for radiation oncology, diagnostic imaging, related fields
+ * med-practice for general practitioners
+ * med-tools contains miscellaneous tools
+ * med-typesetting depends from useful tools for typesetting
+ .
+ Note: All these packages are so called metapackages. This means they are not
+ executable programs, but only links to other packages. This way you will
+ conveniently get all the non-commercial medical software which is available
+ for Debian GNU/Linux.
+
+
+Package: med-bio
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: adun.app, altree, amap-align, autodock, biosquid, blast2, boxshade, dialign, dialign-tx, embassy-domainatrix, embassy-domalign, emboss, exonerate, fastdnaml, fastlink, gamgi, garlic, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, kalign, last-align, loki, mafft, maq, massxpert, melting, mipe, mummer, muscle, mustang, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, perlprimer, phyml, plasmidomics, poa, primer3, probcons, proda, pymol, r-cran-qtl, r-other-bio3d, rasmol, readseq, rnahybrid, seaview, sibsim4, sigma-align, sim4, ssake, t-coffee, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
+Suggests: acedb-other, acedb-other-belvu, acedb-other-dotter, act, agdbnet, alien-hunter, amos-assembler, amoscmp, arb, artemis, asap, autodocktools, axparafit, axpcoords, ballview, bambus, beast-mcmc, big-blast, bio-mauve, blixem, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, clustalw, clustalw-mpi, clustalx, cluster3, coalesce, contralign, coot, copycat, cytoscape, das-proserver, dazzle, decipher, dotter, dotur, ecell, elph, emboss-explorer, emboss-kaptain, est-db, estferret, estscan, exalt, fasta, fastx-toolkit, figaro, finex, fluctuate, forester, galaxy, gbioseq, gbrowse, genesplicer, genetrack, genezilla, genographer, glimmerhmm, gmv, grogui, haploview, hawkeye, hexamer, infernal, jalview, jigsaw, jmol, jtreeview, kempbasu, lamarc, logomat-m, lucy, mage2tab, martj, mauvealigner, maxd, meme, mesquite, migrate, minimus, mira, mirbase, molekel, molphy, mozilla-biofox, mrbayes, msatfinder, mummergpu, murasaki, mview, ncoils, ngila, obo-edit, oligoarrayaux, omegamap, operondb, paml, partigene, patman, pdb2pqr, pfaat, pftools, phpphylotree, phylip, phylographer, phylowin, plink, populations, prank, proalign, profit, prot4est, pyrophosphate-tools, qtlcart, r-ape, r-other-genabel, r-other-mott-happy, raster3d, raxml, rbs-finder, recombine, repeatfinder, reputer, roche454ace2caf, rose, rosetta, samtools, seq-gen, sequenceconverter.app, smile, spice, splitstree, srf, ssaha, staden-io-lib-utils, tacg, taverna, taxinspector, tetra, tm-align, trace2dbest, tracetuner, transtermhp, treeplot, treetool, treevolve, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+
+Package: med-bio-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: bioperl, bioperl-run, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libqsearch-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats
+Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbio-mage-utils-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, libstaden-read-dev, limma, r-cran-rocr, seqan
+Description: Debian Med packages for development of micro-biology applications
+ This metapackage will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
+Package: med-cms
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Suggests: zope-zms
+Description: Debian Med content management systems
+ This metapackage will install packages which are useful to build a
+ content management system for medical care.
+
+Package: med-epi
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: epigrass, r-cran-epi, r-cran-epibasix, r-cran-epitools
+Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance
+Description: Debian Med epidemiology related packages
+ This metapackage will install tools that are useful in epidemiological
+ research. Several packages making use of the GNU R data language for
+ statistical investigation. It might be a good idea to read the paper
+ "A short introduction to R for Epidemiology" at
+ http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
+
+Package: med-imaging
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, amide, ctn, dcmtk, dicomnifti, fslview, gwyddion, imagej, medcon, minc-tools, nifti-bin, python-mvpa, python-nifti, python-nipy, sofa-apps, xmedcon
+Suggests: afni, bioimagesuite, blox, brainvisa, caret, conquest-dicom-server, ctsim, dcm4che, devide, dicom3tools, dicom4j, dicomscope, drjekyll, ecg2png, fiji, fsl, imagemagick, imview, kradview, libgdcm-tools, libvista2, lipsia, maris, mesa-test-tools, micromanager, mni-autoreg, mni-n3, mrisim, odin, opendicom.net, opensourcepacs, piano, pixelmed, pixelmed-dicom-toolkit, pngquant, slicer, via, visit
+Description: Debian Med imaging packages
+ This metapackage will install Debian packages which might be useful in
+ medical image processing.
+ .
+ It installs several packages supporting DICOM (Digital Imaging and
+ Communications in Medicine) which is the de-facto standard for medical
+ image management. The standard defines data structures and services for
+ the exchange of medical images and related information. The latest release
+ has been published in 2008 and consists of 18 parts.
+ .
+ For more information, you can visit the NEMA homepage
+ http://medical.nema.org/ .
+ .
+ The status of the official DICOM base standard plus all the
+ supplements and correction items are summarized at David Clunie's webpage:
+ http://www.dclunie.com/dicom-status/status.html
+ where you'll find direct links to the most recent yearly edition
+ ftp://medical.nema.org/medical/dicom/2008/ .
+
+Package: med-imaging-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cimg-dev, ctn-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti1-dev, libvolpack1-dev, python-mvpa, python-nipy
+Suggests: igstk-examples, insighttoolkit3-examples, libgdcm2-dev, libigstk3-dev, libmni-perllib-perl, libnifti-doc, libvista2-dev, libvtk5, odin, python-libavg, rumba
+Description: Debian Med packages for medical image development
+ This metapackage will install Debian packages which might be useful
+ for developing applications for medical image processing.
+
+Package: med-pharmacy
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: chemtool
+Description: Debian Med packages for pharmaceutical research
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Package: med-physics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: octave3.0, paw, paw++, r-base | r-base-core
+Suggests: biosig, gate, paw-demos
+Description: Debian Med packages for medical physicists
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
+Package: med-practice
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, gnumed-client, gnumed-server, libchipcard-tools
+Suggests: clearhealth, elementalclinic, elexis, freeb, freemed, medintux, mirrormed, mirth, openemr, openpms, openrep, resmedicinae, sqlclinic, tinyheb
+Description: Debian Med packages for practice management
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for practitioners to manage their practice.
+
+Package: med-psychology
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: praat, psignifit, psychopy, python-pyepl, r-cran-foreign, r-cran-psy
+Suggests: visionegg
+Description: Debian Med packages for psychology
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for psychological research.
+
+Package: med-statistics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: r-cran-qvalue, r-cran-randomforest
+Suggests: science-statistics
+Description: Debian Med statistics
+ This metapackage will install packages which are helpful to do statistics
+ with a special focus on tasks in medical care.
+
+Package: med-tools
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cycle, hunspell-de-med, mencal, pondus, wgerman-medical
+Suggests: cl-pubmed, hunspell-en-med, linuxorg-pcal, mssstest, quitcount
+Description: Debian Med several tools
+ This metapackage will install tools for several purposes in health care.
+ Currently it contains some simple programs for Personal Health.
+
+Package: med-typesetting
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: texlive-latex-extra, texlive-science
+Suggests: bibus, kbibtex
+Description: Debian Med support for typesetting and publishing
+ This metapackage will install Debian packages that might be helpful
+ for typesetting and publishing in medical care and structural
+ biology.
+
Added: projects/med/tags/1.3/debian/control.stub
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/control.stub?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/control.stub (added)
+++ projects/med/tags/1.3/debian/control.stub Sat Jun 23 12:46:46 2012
@@ -1,0 +1,21 @@
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7)
+Build-Depends-Indep: blends-dev (>= 0.6.6)
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
+
+Package: med-tasks
+Architecture: all
+Depends: tasksel
+Description: Debian Med tasks for tasksel
+ This package provides Debian Med tasks in tasksel.
+ .
+ These tasks are described in detail at
+ http://debian-med.alioth.debian.org/tasks/
+
Added: projects/med/tags/1.3/debian/copyright
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/copyright?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/copyright (added)
+++ projects/med/tags/1.3/debian/copyright Sat Jun 23 12:46:46 2012
@@ -1,0 +1,5 @@
+This package is Copyright 2004-2009 by Andreas Tille <tille at debian.org>
+
+This software is licensed under the GPL.
+
+On Debian systems, the GPL can be found at /usr/share/common-licenses/GPL.
Added: projects/med/tags/1.3/debian/med-config.postinst.stub
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/med-config.postinst.stub?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/med-config.postinst.stub (added)
+++ projects/med/tags/1.3/debian/med-config.postinst.stub Sat Jun 23 12:46:46 2012
@@ -1,0 +1,7 @@
+#!/bin/sh -e
+
+# if apt-get hook of med-common package remains it might lead to
+# creating user menus twice. So get rid of this not needed file.
+if [ -e /etc/apt/apt.conf.d/90med-common ] ; then
+ rm /etc/apt/apt.conf.d/90med-common
+fi
Added: projects/med/tags/1.3/debian/oldchangelogs/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/bio?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/bio (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/bio Sat Jun 23 12:46:46 2012
@@ -1,0 +1,95 @@
+med-bio (0.5-6) unstable; urgency=low
+
+ * Added depends: ncbi-epcr, r-cran-qtl
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Feb 2004 12:11:37 +0100
+
+med-bio (0.5-5) unstable; urgency=low
+
+ * Added:
+ Depends: loki, tigr-glimmer
+ Suggests: r-base-core
+
+ -- Andreas Tille <tille at debian.org> Wed, 14 Jan 2004 08:31:37 +0100
+
+med-bio (0.5-4) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Depend from further packages:
+ blast2, ncbi-tools-bin, ncbi-tools-x11
+ * Standards-Version: 3.5.9
+ * debian/compat now stores debhelper compatibility version
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Apr 2003 08:21:01 +0200
+
+med-bio (0.5-2) unstable; urgency=low
+
+ * Depend from further packages:
+ bioperl, hmmer, rasmol
+ * Standards-Version: 3.5.8
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Jan 2003 21:37:07 +0100
+
+med-bio (0.5-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Mon, 24 Jun 2002 17:00:19 +0200
+
+med-bio (0.4-3) unstable; urgency=low
+
+ * Added list of dependend packages to package description.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 21:53:41 +0200
+
+med-bio (0.4-2) unstable; urgency=low
+
+ * Added pymol to dependencies.
+ * Introduces /usr/bin/med-bio
+ to give auto-apt a chance to install the package
+ * Manpage for this script.
+ * Remark regarding to the menu entry which was introduced in the last
+ version:
+ The policy violation will be removed and we (Ben Amstrong - Debian-Jr
+ initiator and me) decided to find a better, i.e. user based, menu
+ system.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 20:45:57 +0200
+
+med-bio (0.4-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 12:24:01 +0200
+
+med-bio (0.3-1) unstable; urgency=low
+
+ * Added garlic
+
+ -- Andreas Tille <tille at debian.org> Fri, 19 Apr 2002 15:06:27 +0200
+
+med-bio (0.2-1) unstable; urgency=low
+
+ * Added bugsx
+
+ -- Andreas Tille <tille at debian.org> Sun, 14 Apr 2002 18:44:55 +0200
+
+med-bio (0.1-2) unstable; urgency=low
+
+ * Added biomode, fastdnaml
+
+ -- Andreas Tille <tille at debian.org> Fri, 8 Feb 2002 08:29:38 +0100
+
+med-bio (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132669
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/1.3/debian/oldchangelogs/cms
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/cms?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/cms (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/cms Sat Jun 23 12:46:46 2012
@@ -1,0 +1,6 @@
+med-cms (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #226464
+
+ -- Andreas Tille <tille at debian.org> Tue, 6 Jan 2004 11:03:42 +0100
Added: projects/med/tags/1.3/debian/oldchangelogs/dent
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/dent?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/dent (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/dent Sat Jun 23 12:46:46 2012
@@ -1,0 +1,60 @@
+med-dent (0.5-2) unstable; urgency=low
+
+ * Added French debconf translation
+ Closes: #236301
+ * Reenabled user menu via med_install_helper
+
+ -- Andreas Tille <tille at debian.org> Tue, 9 Mar 2004 09:17:33 +0100
+
+med-dent (0.5-1) unstable; urgency=low
+
+ * Switched to new debconf format (Thanks to
+ Martin Quinson <Martin.Quinson at tuxfamily.org>
+ for the patch.
+ Closes: Ã#234757
+ * Standards-Version: 3.6.1
+ * Depends: debianutils, mozilla-browser | www-browser
+ instead of galeon | www-browser
+ * med-dent script now uses sensible-browser
+ * used debian/install, debian/manpages, debian/compat
+
+ -- Andreas Tille <tille at debian.org> Thu, 26 Feb 2004 08:23:56 +0100
+
+med-dent (0.4-1) unstable; urgency=low
+
+ * Do not depend from Odontolinux! but ask user for the server name which
+ hosts the Odontolinux! server
+ Closes: #167585
+
+ -- Andreas Tille <tille at debian.org> Wed, 25 Dec 2002 11:07:15 +0100
+
+med-dent (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 17:38:44 +0200
+
+med-dent (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Dent menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+ * Depends www-browser
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 17:53:56 +0200
+
+med-dent (0.1-2) unstable; urgency=low
+
+ * move to section misc instead of doc (where it stupidly landed)
+
+ -- Andreas Tille <tille at debian.org> Fri, 22 Feb 2002 12:14:35 +0100
+
+med-dent (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132667
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/1.3/debian/oldchangelogs/imaging
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/imaging?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/imaging (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/imaging Sat Jun 23 12:46:46 2012
@@ -1,0 +1,70 @@
+med-imaging (0.4-4) unstable; urgency=low
+
+ * Removed rumbaview which was removed from Debian
+ closes: #214229
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Oct 2003 20:38:28 +0200
+
+med-imaging (0.4-3) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added minc-tools, medcon, xmedcon
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 10:54:27 +0200
+
+med-imaging (0.4-2) unstable; urgency=low
+
+ * Really *Depends* from med-common, which was just a typo to add
+ it to Suggests - list
+ closes: #151881
+ * Fixes typo in description
+ closes: #152614
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Jul 2002 13:54:32 +0200
+
+med-imaging (0.4-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+ * Forgot to mention newly added ctsim package in package description.
+ * Added ctn to dependencies.
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jun 2002 16:21:14 +0200
+
+med-imaging (0.3-1) unstable; urgency=low
+
+ * Added ctsim to dependencies
+ * Introduces /usr/bin/med-imaging
+ to give auto-apt a chance to install the package
+ * Manpage for this script.
+ * Remark regarding to the menu entry which was introduced in the last
+ version:
+ The policy violation will be removed and we (Ben Amstrong - Debian-Jr
+ initiator and me) decided to find a better, i.e. user based, menu
+ system.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 07:23:05 +0200
+
+med-imaging (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+ * Added some information about rumbaview which is quite sparse in the
+ package itself.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 09:34:32 +0200
+
+med-imaging (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142458
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
Added: projects/med/tags/1.3/debian/oldchangelogs/imaging-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/imaging-dev?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/imaging-dev (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/imaging-dev Sat Jun 23 12:46:46 2012
@@ -1,0 +1,58 @@
+med-imaging-dev (0.3-4) unstable; urgency=low
+
+ * Removed librumba-dev from dependencies because it was removed from Debian
+ closes: #214230
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Oct 2003 20:45:59 +0200
+
+med-imaging-dev (0.3-3) unstable; urgency=low
+
+ * What difference does it make to the dead, the orphans and the homeless,
+ whether the mad destruction is wrought under the name of totalitarianism
+ or the holy name of liberty or democracy?
+ -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War"
+ * Changed dependency from libmdc-dev to libmdc2-dev
+ closes: #190240
+
+ -- Andreas Tille <tille at debian.org> Wed, 23 Apr 2003 13:25:30 +0200
+
+med-imaging-dev (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added libmdc-dev, libminc0-dev
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 11:12:52 +0200
+
+med-imaging-dev (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+ * Added ctn-dev to to dependencies.
+ * "avoids" #150864
+ It does not close the bug because it is an enlightenment bug and so
+ it will be reassigned. But the bug will not show up any more with this
+ package because the menu section was renamed.
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jun 2002 16:18:18 +0200
+
+med-imaging-dev (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:43:59 +0200
+
+med-imaging-dev (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142459
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
Added: projects/med/tags/1.3/debian/oldchangelogs/tools
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/oldchangelogs/tools?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/oldchangelogs/tools (added)
+++ projects/med/tags/1.3/debian/oldchangelogs/tools Sat Jun 23 12:46:46 2012
@@ -1,0 +1,42 @@
+med-tools (0.3-3) unstable; urgency=low
+
+ * Removed dependency on gnutrion
+ closes: #199107
+
+ -- Andreas Tille <tille at debian.org> Sun, 29 Jun 2003 07:45:53 +0200
+
+med-tools (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added gnutrition
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 09:40:43 +0200
+
+med-tools (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 23:21:16 +0200
+
+med-tools (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:45:18 +0200
+
+med-tools (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142901
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/1.3/debian/rules
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/debian/rules?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/debian/rules (added)
+++ projects/med/tags/1.3/debian/rules Sat Jun 23 12:46:46 2012
@@ -1,0 +1,3 @@
+#!/usr/bin/make -f
+
+include /usr/share/blends-dev/rules
Propchange: projects/med/tags/1.3/debian/rules
------------------------------------------------------------------------------
svn:executable = *
Added: projects/med/tags/1.3/menu/bio-dev/biomode.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/biomode.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/biomode.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/biomode.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,11 @@
+BioMode: Emacs mode to edit genetic data
+
+Some information about Biomode from the Debian Med project.
+
+ It provides you several interesting commands to take the antiparallel
+ of a region, convert it using readseq, runs blast on it, etc.
+
+This package is not really installed by the med-bio package but it is
+suggested. That means if you are comfortable with the powerful editor
+Emacs you might wish to install also the biomode package and make use
+of it by typing "M-x biomode".
Added: projects/med/tags/1.3/menu/bio-dev/bioperl.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/bioperl.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/bioperl.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/bioperl.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,13 @@
+Bioperl: Perl tools for computational molecular biology
+
+Some information about Bioperl from the Debian Med project.
+
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules.
+
+The Homepage is http://bio.perl.org/
+
+You can get a good overview by the main manpage:
+
+ man bioperl
Added: projects/med/tags/1.3/menu/bio-dev/libbio-ruby.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/libbio-ruby.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/libbio-ruby.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/libbio-ruby.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,12 @@
+BioRuby tools for computational molecular biology
+
+Some information about libbio-ruby from the Debian Med project.
+
+ BioRuby project aims to implement an integrated environment for
+ Bioinformatics with Ruby language. Design philosophy of the BioRuby library
+ is KISS (keep it simple and stupid) to maximize the usability and the
+ efficiency for biologists as a daily tool. The project was started in Japan
+ and supported by University of Tokyo (Human Genome Center), Kyoto University
+ (Bioinformatics Center) and the Open Bio Foundation.
+
+Homepage: http://www.bioruby.org/
Added: projects/med/tags/1.3/menu/bio-dev/libncbi6-dev.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/libncbi6-dev.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/libncbi6-dev.menu (added)
+++ projects/med/tags/1.3/menu/bio-dev/libncbi6-dev.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,4 @@
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/asntool" needs="X11" \
+ section="Med/Biology development" title="asntool" hints="Biology" icon="/usr/share/pixmaps/asntool.xpm"
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/errhdr" needs="X11" \
+ section="Med/Biology development" title="errhdr" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/1.3/menu/bio-dev/libvibrant6-dev.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/libvibrant6-dev.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/libvibrant6-dev.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/libvibrant6-dev.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,13 @@
+libvibrant6-dev: NCBI libraries for graphic biology applications
+ (development files)
+
+Some information about libvibrant6-dev from the Debian Med project.
+
+ Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
+ biological applications.
+
+The Homepage is http://www.ncbi.nlm.nih.gov/
+
+You can get a good overview by reading
+
+ zless /usr/share/doc/libvibrant6-dev/README.gz
Added: projects/med/tags/1.3/menu/bio-dev/mcl.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/mcl.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/mcl.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/mcl.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,33 @@
+MCL: Markov Cluster algorithm
+
+Some information about mcl from the Debian Med project.
+
+ The MCL package is an implementation of the MCL algorithm, and offers
+ utilities for manipulating sparse matrices (the essential data
+ structure in the MCL algorithm) and conducting cluster experiments.
+
+ MCL is currently being used in sciences like biology (protein family
+ detection, genomics), computer sciense (node clustering in
+ Peer-to-Peer networks), and linguistics (text analysis).
+
+ Homepage: http://micans.org/mcl/
+
+An overview about the various tools are given by the following manpages:
+
+ man mcx
+ man clmimac
+ man clmmate
+ man clmmeet
+ man clmformat
+ man clmdist
+ man clminfo
+ man mcxconvert
+ man mcxassemble
+ man mcxmap
+ man mcxsubs
+ man mcxarray
+ man mcxdeblast
+ man mclblastline
+ man mcl
+ man clmresidue
+ man mclpipeline
Added: projects/med/tags/1.3/menu/bio-dev/python-biopython.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio-dev/python-biopython.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio-dev/python-biopython.txt (added)
+++ projects/med/tags/1.3/menu/bio-dev/python-biopython.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,18 @@
+Python library for bioinformatics
+
+Some information about python-biopython from the Debian Med project.
+
+ The Biopython Project is an international association
+ of developers of freely available Python tools for
+ computational molecular biology.
+
+ It is a distributed collaborative effort to develop Python
+ libraries and applications which address the needs of
+ current and future work in bioinformatics. The source code
+ is made available under the Biopython License, which is
+ extremely liberal and compatible with almost every license
+ in the world. We work along with the Open Bioinformatics
+ Foundation, who generously provide web and CVS space for
+ the project.
+
+Homepage: http://biopython.org/
Added: projects/med/tags/1.3/menu/bio/blast2.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/blast2.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/blast2.menu (added)
+++ projects/med/tags/1.3/menu/bio/blast2.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,29 @@
+# The lot of entries just blast the menu to much
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/bl2seq" needs="X11" \
+ section="Med/Biology/Blast2" title="bl2seq" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blast2" needs="X11" \
+ section="Med/Biology/Blast2" title="blast2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastall" needs="X11" \
+ section="Med/Biology/Blast2" title="blastall" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastcl3" needs="X11" \
+ section="Med/Biology/Blast2" title="blastcl3" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastclust" needs="X11" \
+ section="Med/Biology/Blast2" title="blastclust" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastpgp" needs="X11" \
+ section="Med/Biology/Blast2" title="blastpgp" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/copymat" needs="X11" \
+ section="Med/Biology/Blast2" title="copymat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastacmd" needs="X11" \
+ section="Med/Biology/Blast2" title="fastacmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/formatdb" needs="X11" \
+ section="Med/Biology/Blast2" title="formatdb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/impala" needs="X11" \
+ section="Med/Biology/Blast2" title="impala" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makemat" needs="X11" \
+ section="Med/Biology/Blast2" title="makemat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/megablast" needs="X11" \
+ section="Med/Biology/Blast2" title="megablast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/rpsblast" needs="X11" \
+ section="Med/Biology/Blast2" title="rpsblast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/seedtop" needs="X11" \
+ section="Med/Biology/Blast2" title="seedtop" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/1.3/menu/bio/boxshade.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/boxshade.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/boxshade.txt (added)
+++ projects/med/tags/1.3/menu/bio/boxshade.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,12 @@
+Pretty-printing of multiple sequence alignments
+
+Some information about boxshade from the Debian Med project.
+
+ Boxshade reads a sequence alignment as input (e.g. from ClustalW) and
+ outputs files that may be incorporated to text processing software
+ (TeX via xfig, Word and OpenOffice via RTF). The post script format
+ is also supported.
+
+See also: man boxshade
+
+Homepage: http://www.ch.embnet.org/software/BOX_form.html
Added: projects/med/tags/1.3/menu/bio/fastdnaml.html
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/fastdnaml.html?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/fastdnaml.html (added)
+++ projects/med/tags/1.3/menu/bio/fastdnaml.html Sat Jun 23 12:46:46 2012
@@ -1,0 +1,44 @@
+<html>
+<head>
+<title>Construction of Phylogenetic Trees</title>
+<meta name="author" content="Andreas Tille" />
+</head>
+<body>
+<h2>FastDNAml: Construction of Phylogenetic Trees</h2>
+
+<h3>Some information about fastDNAml from the Debian Med project.</h3>
+
+<h4>fastdnaml provides tools for construction of phylogenetic trees of DNA sequences</h4>
+
+<quote>
+ fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+ (part of his PHYLIP package). Users should consult the documentation for
+ DNAML before using this program.
+ fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+ faster and using less memory, so that larger trees and/or more bootstrap
+ replicates become tractable. Much of fastDNAml is merely a recoding of the
+ PHYLIP 3.3 DNAML program from PASCAL to C.
+</quote>
+
+<h4>For more detailed information see</h4>
+
+<example>
+ man fastDNAml
+ man fastDNAml-util
+ view /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt.gz
+</example>
+
+ or test the examples under
+
+<example>
+ /usr/share/doc/fastdnaml/examples
+</example>
+
+ using the Makefile provided under
+
+<example>
+ /usr/share/doc/fastdnaml/examples/tests
+</example>
+</body>
+</html>
+
Added: projects/med/tags/1.3/menu/bio/fastlink.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/fastlink.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/fastlink.txt (added)
+++ projects/med/tags/1.3/menu/bio/fastlink.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,14 @@
+FastLink: Faster Pedigree
+
+Some information about fastlink from the Debian Med project.
+
+ A faster version of pedigree programs of Linkage
+ Fastlink is much faster than the original Linkage but does not
+ implement all the programs.
+
+Unfortunately there is no manpage for the included tools which are
+ ilink, linkmap, lodscore, mlink
+
+Extensive documentation inclusive PostScript formatted papers are provided under
+
+ /usr/share/doc/fastlink
Added: projects/med/tags/1.3/menu/bio/gff2aplot.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/gff2aplot.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/gff2aplot.txt (added)
+++ projects/med/tags/1.3/menu/bio/gff2aplot.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,11 @@
+Pair-wise alignment-plots for genomic sequences in PostScript
+
+Some information about gff2aplot from the Debian Med project.
+
+ A program to visualize the alignment of two genomic sequences together with
+ their annotations. From GFF-format input files it produces PostScript figures
+ for that alignment.
+
+See also: man gff2aplot
+
+Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Added: projects/med/tags/1.3/menu/bio/gff2ps.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/gff2ps.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/gff2ps.txt (added)
+++ projects/med/tags/1.3/menu/bio/gff2ps.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,16 @@
+Produce PostScript graphical output from GFF-files
+
+Some information about gff2ps from the Debian Med project.
+
+ gff2ps is a script program developed with the aim of converting gff-formatted
+ records into high quality one-dimensional plots in PostScript. Such plots
+ maybe useful for comparing genomic structures and to visualizing outputs from
+ genome annotation programs.
+ It can be used in a very simple way, because it assumes that the GFF file
+ itself carries enough formatting information, but it also allows through a
+ number of options and/or a configuration file, for a great degree of
+ customization.
+
+See also: man gff2ps
+
+Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
Added: projects/med/tags/1.3/menu/bio/glimmer.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/glimmer.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/glimmer.txt (added)
+++ projects/med/tags/1.3/menu/bio/glimmer.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,32 @@
+Tigr Glimmer: Gene detection in archea and bacteria
+
+Some information about tigr-glimmer from the Debian Med project.
+
+ Developed by the TIGR institute this software detects coding sequences in
+ bacteria and archea.
+
+ Glimmer is a system for finding genes in microbial DNA, especially the
+ genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
+ Markov Modeler) uses interpolated Markov models (IMMs) to identify the
+ coding regions and distinguish them from noncoding DNA.
+
+ Homepage: http://www.tigr.org/software/glimmer/
+
+An overview about the various tools are given by the following manpages:
+
+ man glimmer2 (start with this)
+ man build-icm
+ man extract
+ man long-orfs
+
+More or less simple syntax help without detailed information is given by
+
+ man adjust
+ man anomaly
+ man check
+ man codon-usage
+ man compare-lists
+ man generate
+ man get-len
+ man run-glimmer2
+ man get-putative
Added: projects/med/tags/1.3/menu/bio/hmmer.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/hmmer.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/hmmer.txt (added)
+++ projects/med/tags/1.3/menu/bio/hmmer.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+Hmmer: Biological sequence analysis using profile hidden Markov models
+
+Some information about Hmmer from the Debian Med project.
+
+ Hmmer is a suite of programs which use profile hidden Markov models
+ (profile HMMs) to model the primary structure consensus of a family of
+ protein or nucleic acid sequences.
+
+Homepage: http://hmmer.wustl.edu/
+
+You can get a good overview by the main manpage:
+
+ man hmmer
+
+The Hmmer users guide is available at
+
+ http://localhost/doc/hmmer/hmmer-html/index.html
Added: projects/med/tags/1.3/menu/bio/loki.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/loki.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/loki.txt (added)
+++ projects/med/tags/1.3/menu/bio/loki.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+Loki: MCMC linkage analysis on general pedigrees
+
+Some information about Loki from the Debian Med project.
+
+ Performs Markov chain Monte Carlo multipoint linkage analysis on large,
+ complex pedigrees. The current package supports analyses on quantitative
+ traits only, although this restriction will be lifted in later versions.
+ Joint estimation of QTL number, position and effects uses Reversible Jump
+ MCMC. It is also possible to perform affected only IBD sharing analyses.
+
+ Homepage: http://loki.homeunix.net.
+
+You can get a good overview by the main manpage:
+
+ man loki
+
+It is suggested to install the loki-doc package.
Added: projects/med/tags/1.3/menu/bio/mipe.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/mipe.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/mipe.txt (added)
+++ projects/med/tags/1.3/menu/bio/mipe.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,44 @@
+Tools to store PCR-derived data
+
+Some information about mipe from the Debian Med project.
+
+ MIPE provides a standard format to exchange and/or storage of all
+ information associated with PCR experiments using a flat text file. This will:
+ * allow for exchange of PCR data between researchers/laboratories
+ * enable traceability of the data
+ * prevent problems when submitting data to dbSTS or dbSNP
+ * enable the writing of standard scripts to extract data (e.g. a
+ list of PCR primers, SNP positions or haplotypes for different animals)
+
+ Although this tool can be used for data storage, it's primary focus
+ should be data exchange. For larger reporisitories, relational databases
+ are more appropriate for storage of these data. The MIPE format could
+ then be used as a standard format to import into and/or export from
+ these databases.
+
+Homepage: http://mipe.sourceforge.net
+
+You should also read the relevant man pages:
+
+ man mipe06to07
+ man mipe08to09
+ man mipe0_9to1_0
+ man mipe2dbSTS
+ man mipe2fas
+ man mipe2html
+ man mipe2pcroverview
+ man mipe2pcrprimers
+ man mipe2putativesbeprimers
+ man mipe2sbeprimers
+ man mipe2snps
+ man mipeCheckSanity
+ man removePcrFromMipe
+ man removeSbeFromMipe
+ man sbe2mipe
+ man snp2mipe
+ man snpPosOnDesign
+ man snpPosOnSource
+ man csv2mipe
+ man genotype2mipe
+ man mipe2genotypes
+ man removeSnpFromMipe
Added: projects/med/tags/1.3/menu/bio/molphy.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/molphy.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/molphy.txt (added)
+++ projects/med/tags/1.3/menu/bio/molphy.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+Some information about MolPhy from the Debian Med project.
+
+Molphy is an extensive set of tools for MOLecular PHYlogenetics. You can
+get a first overview by the two manpages
+
+ man protml
+ man mollist
+
+For further reading the files in
+
+ /usr/share/doc/molphy
+
+are suggested. Moreover you can find several examples in
+
+ /usr/share/doc/molphy/examples/tests/
+
+which contains a makefile to give you an idea how to call the MolPhy tools.
Added: projects/med/tags/1.3/menu/bio/muscle.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/muscle.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/muscle.txt (added)
+++ projects/med/tags/1.3/menu/bio/muscle.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,39 @@
+Multiple alignment program of protein sequences
+
+Some information about Muscle from the Debian Med project.
+
+MUSCLE is a multiple alignment program for protein sequences. MUSCLE
+stands for multiple sequence comparison by log-expectation. In the
+authors tests, MUSCLE achieved the highest scores of all tested
+programs on several alignment accuracy benchmarks, and is also one of
+the fastest programs out there.
+
+Homepage: http://www.drive5.com/muscle
+
+Basic usage
+
+ muscle -in <inputfile> -out <outputfile>
+
+Common options (for a complete list please see the User Guide):
+
+ -in <inputfile> Input file in FASTA format (default stdin)
+ -out <outputfile> Output alignment in FASTA format (default stdout)
+ -diags Find diagonals (faster for similar sequences)
+ -maxiters <n> Maximum number of iterations (integer, default 16)
+ -maxhours <h> Maximum time to iterate in hours (default no limit)
+ -maxmb <m> Maximum memory to allocate in Mb (default 80% of RAM)
+ -html Write output in HTML format (default FASTA)
+ -msf Write output in GCG MSF format (default FASTA)
+ -clw Write output in CLUSTALW format (default FASTA)
+ -clwstrict As -clw, with 'CLUSTAL W (1.81)' header
+ -log[a] <logfile> Log to file (append if -loga, overwrite if -log)
+ -quiet Do not write progress messages to stderr
+ -stable Output sequences in input order (default is -group)
+ -group Group sequences by similarity (this is the default)
+ -version Display version information and exit
+
+Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
+Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
+Fastest possible (nucleotides): -maxiters 1 -diags
+
+See also: man muscle
Added: projects/med/tags/1.3/menu/bio/ncbi-epcr.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/ncbi-epcr.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/ncbi-epcr.txt (added)
+++ projects/med/tags/1.3/menu/bio/ncbi-epcr.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,16 @@
+NCBI-EPCR: Tool to test a DNA sequence for the presence of sequence tagged sites
+
+Some information about NCBI-Tools-Bin from the Debian Med project.
+
+ Electronic PCR feature to test a DNA sequence for the presence of
+ sequence tagged sites. e-PCR looks for STSs in DNA sequences by
+ searching for subsequences that closely match the PCR primers and have
+ the correct order, orientation, and spacing that they could plausibly
+ prime the amplification of a PCR product of the correct molecular weight
+ (Schuler, Genome Research 7:541-50, 1997).
+
+ Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi
+
+ For further information try:
+
+ man e-PCR
Added: projects/med/tags/1.3/menu/bio/ncbi-tools-bin.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/ncbi-tools-bin.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/ncbi-tools-bin.menu (added)
+++ projects/med/tags/1.3/menu/bio/ncbi-tools-bin.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,43 @@
+# The lot of entries just blast the menu to much
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2asn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2ff" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2ff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2gb" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2gb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2xml" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2xml" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asndhuff" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asndhuff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/checksub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="checksub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/debruijn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="debruijn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/entrcmd" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="entrcmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fa2htgs" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="fa2htgs" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastamerge" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="fastamerge" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/findspl" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="findspl" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gbseqget" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="gbseqget" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getfeat" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getfeat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getmesh" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getmesh" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getpub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gil2bin" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="gil2bin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/idfetch" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="idfetch" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/indexpub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="indexpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makeset" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="makeset" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/tbl2asn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="tbl2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/vecscreen" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="vecscreen" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/1.3/menu/bio/ncbi-tools-x11.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/ncbi-tools-x11.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/ncbi-tools-x11.menu (added)
+++ projects/med/tags/1.3/menu/bio/ncbi-tools-x11.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,14 @@
+?package(ncbi-tools-x11):command="/usr/bin/Cn3D-3.0" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Cn3D-3.0" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/Nentrez" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Entrez" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/Psequin" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Sequin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/ddv" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="ddv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/entrez2" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="entrez2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/netentcf" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Entrez net config" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/udv" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="udv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/1.3/menu/bio/phylip.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/phylip.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/phylip.txt (added)
+++ projects/med/tags/1.3/menu/bio/phylip.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,26 @@
+Some information about Phylip from the Debian Med project.
+
+ A package of programs for inferring phylogenies.
+
+ The PHYLogeny Inference Package is a package of programs for inferring
+ phylogenies (evolutionary trees) from sequences.
+ Methods that are available in the package include parsimony, distance
+ matrix, and likelihood methods, including bootstrapping and consensus
+ trees. Data types that can be handled include molecular sequences, gene
+ frequencies, restriction sites, distance matrices, and 0/1 discrete
+ characters.
+
+If you call phylip in a text console you get some help:
+
+ Usage: /usr/bin/phylip <program>
+ Existing programs are:
+ clique dnacomp dnamlk dollop drawtree kitsch penny retree
+ consense dnadist dnamove dolmove factor mix protdist seqboot
+ contml dnainvar dnapars dolpenny fitch move protpars
+ contrast dnaml dnapenny drawgram gendist neighbor restml
+
+which is quite the same information as the Debian manpage of phylip
+contains.
+There is extensive documentation at /usr/share/doc/phylip and some
+examples in the examples dir at this location.
+
Added: projects/med/tags/1.3/menu/bio/poa.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/poa.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/poa.txt (added)
+++ projects/med/tags/1.3/menu/bio/poa.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,18 @@
+Partial Order Alignment for multiple sequence alignment
+
+Some information about t-coffee from the Debian Med project.
+
+ POA is Partial Order Alignment, a fast program for multiple sequence
+ alignment (MSA) in bioinformatics. Its advantages are speed,
+ scalability, sensitivity, and the superior ability to handle branching
+ / indels in the alignment. Partial order alignment is an approach to
+ MSA, which can be combined with existing methods such as progressive
+ alignment. POA optimally aligns a pair of MSAs and which therefore can
+ be applied directly to progressive alignment methods such as CLUSTAL.
+ For large alignments, Progressive POA is 10-30 times faster than
+ CLUSTALW. POA is published in Bioinformatics. 2004 Jul
+ 10;20(10):1546-56.
+
+See also: man poa
+
+Homepage: http://www.bioinformatics.ucla.edu/poa
Added: projects/med/tags/1.3/menu/bio/r-cran-qtl.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/r-cran-qtl.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/r-cran-qtl.txt (added)
+++ projects/med/tags/1.3/menu/bio/r-cran-qtl.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,23 @@
+r-cran-qtl: GNU R package for genetic marker linkage analysis
+
+Some information about r-cran-qtl from the Debian Med project.
+
+ R/qtl is an extensible, interactive environment for
+ mapping quantitative trait loci (QTLs) in experimental crosses. It is
+ implemented as an add-on-package for the freely available and widely used
+ statistical language/software R (see http://www.r-project.org). The
+ user will benefit from the seamless integration of the QTL mapping
+ software into a general statistical analysis program.
+
+ The current version of R/qtl includes facilities for estimating
+ genetic maps, identifying genotyping errors, and performing single-QTL
+ genome scans and two-QTL, two-dimensional genome scans, by interval
+ mapping (with EM algorithm), Haley-Knott regression, and multiple
+ imputation. All of this may be done in the presence of covariates
+ (such as sex, age or treatment). The fit of higher-order QTL models,
+ with sophisticated techniques for model comparisons and model search,
+ will be incorporated soon.
+
+More information can be found at
+
+ Homepage: http://www.biostat.jhsph.edu/~kbroman/qtl/index.html
Added: projects/med/tags/1.3/menu/bio/readseq.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/readseq.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/readseq.txt (added)
+++ projects/med/tags/1.3/menu/bio/readseq.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+ReadSeq: Conversion between sequence formats
+
+Some information about readseq from the Debian Med project.
+
+ Reads and writes nucleic/protein sequences in various formats. Data
+ files may have multiple sequences. Readseq is particularly useful as it
+ automatically detects many sequence formats, and converts between them.
+
+Please read the manual for this program by
+
+ man readseq
+
+To test the program you could also test the examples under
+
+ /usr/share/doc/readseq/tests
+
+using the provided Makefile.
Added: projects/med/tags/1.3/menu/bio/sim4.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/sim4.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/sim4.txt (added)
+++ projects/med/tags/1.3/menu/bio/sim4.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,25 @@
+Tool for aligning cDNA and genomic DNA
+
+Some information about sim4 from the Debian Med project.
+
+ sim4 is a similarity-based tool for aligning an expressed DNA sequence
+ (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end
+ matches when the two input sequences overlap at one end (i.e., the start of
+ one sequence overlaps the end of the other).
+
+ sim4 employs a blast-based technique to first determine the basic matching
+ blocks representing the "exon cores". In this first stage, it detects all
+ possible exact matches of W-mers (i.e., DNA words of size W) between the two
+ sequences and extends them to maximal scoring gap-free segments. In the
+ second stage, the exon cores are extended into the adjacent as-yet-unmatched
+ fragments using greedy alignment algorithms, and heuristics are used to favor
+ configurations that conform to the splice-site recognition signals (GT-AG,
+ CT-AC). If necessary, the process is repeated with less stringent parameters
+ on the unmatched fragments.
+
+
+Homepage: http://www.bx.psu.edu/miller_lab/
+
+Please read the man page of this project:
+
+ man sim4
Added: projects/med/tags/1.3/menu/bio/t-coffee.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/bio/t-coffee.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/bio/t-coffee.txt (added)
+++ projects/med/tags/1.3/menu/bio/t-coffee.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+Multiple Sequence Alignment
+
+Some information about t-coffee from the Debian Med project.
+
+ T-Coffee is a multiple sequence alignment package. Given a set of
+ sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+ alignment. Version 2.00 and higher can mix sequences and structures.
+
+ T-Coffee allows the combination of a collection of multiple/pairwise,
+ global or local alignments into a single model. It also allows to
+ estimate the level of consistency of each position within the new
+ alignment with the rest of the alignments. See the pre-print for more
+ information
+
+See also: man t_coffee
+
+Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
Added: projects/med/tags/1.3/menu/cms/zope-zms.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/cms/zope-zms.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/cms/zope-zms.txt (added)
+++ projects/med/tags/1.3/menu/cms/zope-zms.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,24 @@
+zope-zms: Content management for science, technology and medicine
+
+Some information about Zope ZMS from the Debian Med project.
+
+ ZMS (Zope based Content Management for Science, Technology and Medicine)
+ is a ready to use solution for efficient electronic publishing. An easy
+ to handle graphical user interface for editors and flexible modelling
+ features (multiple languages, Metadata, content objects, XML
+ import/export, workflow etc.) allow an optimum of productivity: A
+ basic configuration to start with can be created with a few mouse clicks.
+
+ ZMS is perfectly suitable for hospitals, research institutions, NGOs
+ and small to medium-size international companies.
+
+ The ZMS concept is based on a consulting approach for the rational
+ publishing on the internet: the professional user is able to pursue
+ a consequently efficiency oriented producing base with the ZMS software
+ and can hereby also achieve important economic results in the so-called
+ low budget area. The modulation possibilities of the ZMS components and
+ the experienced producing steps makes out of ZMS an incomparable fast tool.
+
+ Homepage: http://www.zms-publishing.com/
+
+ Read /usr/share/doc/zope-zms/README.Debian for the first steps.
Added: projects/med/tags/1.3/menu/imaging-dev/ctn-dev.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging-dev/ctn-dev.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging-dev/ctn-dev.txt (added)
+++ projects/med/tags/1.3/menu/imaging-dev/ctn-dev.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,15 @@
+CTN Development: CTN-Dicom support
+
+Some information about ctn from the Debian Med project.
+
+The ctn package provides runtime files for Central Test Node,
+a DICOM implementation.
+DICOM is the standard for image storage, annotation, and networking.
+It is used widely for medical imaging.
+
+This is the development package.
+
+For further information have a look into the extensive documentation
+which is in the Debian package ctn-doc.
+
+The homepage is http://www.erl.wustl.edu/DICOM/ctn.html.
Added: projects/med/tags/1.3/menu/imaging-dev/libgtkimreg-dev.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging-dev/libgtkimreg-dev.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging-dev/libgtkimreg-dev.txt (added)
+++ projects/med/tags/1.3/menu/imaging-dev/libgtkimreg-dev.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,12 @@
+Imreg Development: Image Sequences Development Support
+
+Some information about libgtkimreg-dev from the Debian Med project.
+
+Please read
+
+ man gtkimreg
+ man gtkimmov
+
+for a detailed description for cutting and moving sets of images.
+A complex example of the usage of these libraries is the image viewer
+paul.
Added: projects/med/tags/1.3/menu/imaging-dev/libmdc2-dev.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging-dev/libmdc2-dev.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging-dev/libmdc2-dev.txt (added)
+++ projects/med/tags/1.3/menu/imaging-dev/libmdc2-dev.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,13 @@
+MedCon Development: Medical Image Conversion development
+
+Some information about libmdc-dev from the Debian Med project.
+
+We are sorry that we can not present a more detailed description to this
+development package. We suggest further reading at the xmedcon homepage
+
+ http://xmedcon.sourceforge.net
+
+because it belongs to the XMedCon package.
+
+The following manpages might help you in getting started:
+ xmedcon-config medcon m-gif m-inw m-acr m-ecat m-anlz m-intf
Added: projects/med/tags/1.3/menu/imaging-dev/libminc0-dev.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging-dev/libminc0-dev.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging-dev/libminc0-dev.txt (added)
+++ projects/med/tags/1.3/menu/imaging-dev/libminc0-dev.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,12 @@
+MINC Development: MNI medical image format development
+
+Some information about libminc0-dev from the Debian Med project.
+
+The best way to get started with this development package is to read
+
+ http://localhost/doc/libminc0-dev/
+
+if you have a working webserver installed on your local machine or just
+browse
+
+ /usr/share/doc/libminc0-dev
Added: projects/med/tags/1.3/menu/imaging/ctn.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging/ctn.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging/ctn.txt (added)
+++ projects/med/tags/1.3/menu/imaging/ctn.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,25 @@
+CTN: Runtime files for Central Test Node, a DICOM implementation
+
+Some information about ctn from the Debian Med project.
+
+The ctn package provides runtime files for Central Test Node,
+a DICOM implementation.
+DICOM is the standard for image storage, annotation, and networking.
+It is used widely for medical imaging.
+
+Information about the tools which are provided can be obtained by
+
+ man dcm_ctnto10
+ man dcm_diff
+ man dcm_dump_element
+ man dcm_dump_file
+ man dcm_make_object
+ man dcm_map_to_8
+ man dcm_rm_element
+ man dcm_verify
+ man dcm_add_fragments
+ man dcm_create_object
+
+The homepage is http://www.erl.wustl.edu/DICOM/ctn.html.
+
+Extensive documentation is provided in the Debian package ctn-doc.
Added: projects/med/tags/1.3/menu/imaging/dcmtk.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging/dcmtk.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging/dcmtk.txt (added)
+++ projects/med/tags/1.3/menu/imaging/dcmtk.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,58 @@
+The OFFIS DICOM toolkit command line utilities
+
+Some information about dcmtk from the Debian Med project.
+
+ DCMTK includes a collection of libraries and applications for examining,
+ constructing and converting DICOM image files, handling offline media,
+ sending and receiving images over a network connection, as well as
+ demonstrative image storage and worklist servers.
+
+Homepage: http://dicom.offis.de/
+
+The package contains a set of utilities. They are described in the
+relevant man pages which are:
+
+ man dbregimg
+ man dcm2pnm
+ man dcm2xml
+ man dcmcjpeg
+ man dcmconv
+ man dcmcrle
+ man dcmdjpeg
+ man dcmdrle
+ man dcmdspfn
+ man dcmdump
+ man dcmftest
+ man dcmgpdir
+ man dcmj2pnm
+ man dcmmkcrv
+ man dcmmkdir
+ man dcmmklut
+ man dcmodify
+ man dcmp2pgm
+ man dcmprscp
+ man dcmprscu
+ man dcmpschk
+ man dcmpsmk
+ man dcmpsprt
+ man dcmpsrcv
+ man dcmpssnd
+ man dcmquant
+ man dcmscale
+ man dcmsign
+ man dcod2lum
+ man dconvlum
+ man dsr2html
+ man dsr2xml
+ man dsrdump
+ man dump2dcm
+ man echoscu
+ man findscu
+ man imagectn
+ man movescu
+ man storescp
+ man storescu
+ man ti
+ man wlmscpfs
+ man xml2dcm
+ man xml2dsr
Added: projects/med/tags/1.3/menu/imaging/medcon.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging/medcon.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging/medcon.txt (added)
+++ projects/med/tags/1.3/menu/imaging/medcon.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+MedCon: MEDical image (DICOM, ECAT, ...) CONversion tool
+
+Some information about medcon from the Debian Med project.
+
+The homepage is at
+
+ http://xmedcon.sourceforge.net
+
+There exists a xmedcon tool which provides a nice graphical interface
+and might be a good start for beginners.
+
+Alternatively you can type
+
+ man medcon
+
+to learn how to use medcon.
+
Added: projects/med/tags/1.3/menu/imaging/minc-tools.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging/minc-tools.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging/minc-tools.txt (added)
+++ projects/med/tags/1.3/menu/imaging/minc-tools.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,29 @@
+MINC Tools: MNI medical image format tools
+
+Some information about minc-tools from the Debian Med project.
+
+ The Minc file format is a highly flexible medical image file format
+ built on top of the NetCDF generalized data format. The format is
+ simple, self-describing, extensible, portable and N-dimensional, with
+ programming interfaces for both low-level data access and high-level
+ volume manipulation. On top of the libraries is a suite of generic
+ image-file manipulation tools. The format, libraries and tools are
+ designed for use in a medical-imaging research environment : they are
+ simple and powerful and make no attempt to provide a pretty interface
+ to users.
+
+The best way to start using minc-tools is to read the document
+
+ /usr/share/doc/minc-tools/GETTING_STARTED
+
+A reasonable resource of information is
+
+ http://www.nmr.mgh.harvard.edu/~rhoge/minc/
+
+The following manpages are available for the MINC tools suite:
+
+ mincaverage minccalc mincconcat minccopy mincdiff mincedit mincexpand
+ mincextract mincheader mincinfo mincmakescalar mincmakevector mincmath
+ mincresample mincreshape mincstats invert_raw_image mincview mincwindow
+ rawtominc xfmconcat xfminvert voxeltoworld minc_modify_header minclookup
+ minctoraw transformtags worldtovoxel
Added: projects/med/tags/1.3/menu/imaging/nifti-bin.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/imaging/nifti-bin.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/imaging/nifti-bin.txt (added)
+++ projects/med/tags/1.3/menu/imaging/nifti-bin.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,17 @@
+Tool for reading and writing NIfTI-1 MRI and fMRI brain images
+
+Some information about nifti-bin from the Debian Med project.
+
+ Niftilib is a set of i/o libraries for reading and writing files in the
+ NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical
+ image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI)
+ brain images.
+
+Please read:
+ man nifti_tool
+ man nifti_stats
+ man nifti1_test
+
+Further reading:
+ http://niftilib.sourceforge.net/
+ http://nifti.nimh.nih.gov/
Added: projects/med/tags/1.3/menu/physics/octave.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/physics/octave.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/physics/octave.menu (added)
+++ projects/med/tags/1.3/menu/physics/octave.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,4 @@
+?package(octave2.1):needs="text" \
+ section="Med/Physics" \
+ title="Octave (2.1)" \
+ command="/usr/bin/octave2.1"
Added: projects/med/tags/1.3/menu/physics/r-base.menu
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/physics/r-base.menu?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/physics/r-base.menu (added)
+++ projects/med/tags/1.3/menu/physics/r-base.menu Sat Jun 23 12:46:46 2012
@@ -1,0 +1,4 @@
+?package(r-base-core):needs="text" \
+ section="Med/Physics" \
+ title="GNU R" \
+ command="/usr/bin/R"
Added: projects/med/tags/1.3/menu/tools/mencal.txt
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/menu/tools/mencal.txt?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/menu/tools/mencal.txt (added)
+++ projects/med/tags/1.3/menu/tools/mencal.txt Sat Jun 23 12:46:46 2012
@@ -1,0 +1,10 @@
+MenCal: Menstruation Calendar
+
+Some information about mencal from the Debian Med project.
+
+Please read
+
+ man mencal
+
+for a detailed description of options and the configuration file of the
+menstruation calendar. It is intended to be called from a text console.
Added: projects/med/tags/1.3/tasks.ctl
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks.ctl?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks.ctl (added)
+++ projects/med/tags/1.3/tasks.ctl Sat Jun 23 12:46:46 2012
@@ -1,0 +1,15 @@
+priority-high:bio
+priority-high:bio-dev
+priority-low:cms
+priotity-none:data
+priority-high:epi
+priotity-none:his
+priority-high:imaging
+priority-high:imaging-dev
+priotity-none:laboratory
+priority-high:pharmacy
+priority-high:physics
+priority-high:practice
+priority-high:statistics
+priority-med:tools
+priority-med:typesetting
Added: projects/med/tags/1.3/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/bio?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/bio (added)
+++ projects/med/tags/1.3/tasks/bio Sat Jun 23 12:46:46 2012
@@ -1,0 +1,2920 @@
+Task: Biology
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+
+X-Begin-Category: Phylogenetic analysis
+
+Depends: altree, fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+
+Depends: treeviewx
+X-Published-Authors: FIXME
+X-Published-Title: FIXME
+Published-In: Computer Applications in the Bioscience 12:357-358
+Published-Year: 1996
+
+X-End-Category: Phylogenetic analysis
+
+Depends: molphy, phylip, treetool
+Why: Phylogenetic analysis (Non-free, thus only suggested).
+
+Depends: fastlink, loki, plink, r-cran-qtl
+Why: Genetics
+
+X-Begin-Category: Sequence alignments and related programs.
+
+Depends: amap-align, blast2, boxshade, gff2aplot, hmmer, kalign, mafft, mummer, muscle, sim4, sibsim4, t-coffee, wise, exonerate
+
+Depends: dialign
+Published-Authors: Burkhard Morgenstern
+Published-In: Bioinformatics 15(3):211-218
+Published-Year: 1999
+
+Depends: dialign-tx
+Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
+Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
+Published-In: Algorithms for Molecular Biology 3:6
+Published-Year: 2008
+
+Depends: poa
+Published-Authors: Christopher Lee
+X-Comment: I hope the Copyright owner is the Author of the publication. Please FIX it if I'm wrong!!!
+Published-In: Bioinformatics 10;20(10):1546-1556.
+Published-Year: 2004
+
+Depends: probcons
+Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
+Published-In: Genome Research 15: 330-340
+Published-Year: 2005
+
+Depends: proda
+Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
+Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
+Published-In: Nucleic Acids Research 34(20), 5932-5942
+Published-Year: 2006
+
+Depends: seaview
+Published-Authors: N. Galtier, M. Gouy, C. Gautier
+Published-Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny
+Published-In: Comput. Applic. Biosci. 12:543-548
+Published-Year: 1996
+
+Depends: sigma-align
+X-Published-Authors: FIXME
+X-Published-Title: FIXME
+Published-In: BMC Bioinformatics 16;7:143
+Published-Year: 2006
+
+Depends: emboss, embassy-domalign, embassy-domainatrix
+Suggests: emboss-explorer
+Why: The EMBOSS sequence analysis suite and its galaxy.
+
+Depends: arb, clustalx
+Why: Sequence alignments and related programs (Non-free, thus only suggested).
+
+Depends: clustalw | clustalw-mpi
+X-Published-Authors: M. Larkin, et al.
+X-Published-Title: Clustal W and Clustal X version 2.0
+Published-In: Bioinformatics 23(21):2947-2948
+Published-Year: 2007
+
+X-End-Category: Sequence alignments and related programs.
+
+Depends: last-align, maq, ssake, velvet
+Why: Tools related to high-throughput sequencing.
+
+X-Begin-Category: Analysis of RNA sequences.
+
+Depends: infernal
+Published-Authors: E. P. Nawrocki, S. R. Eddy
+Published-Title: Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
+Published-In: PLoS Comput. Biol. 3:e56
+Published-Year: 2007
+
+Depends: rnahybrid
+Published-Authors: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, Robert Giegerich
+Published-Title: Fast and effective prediction of microRNA/target duplexes RNA
+Published-In: 10:1507-1517
+Published-Year: 2004
+
+X-End-Category: Analysis of RNA sequences.
+
+Depends: adun.app, garlic, gamgi, gdpc, ghemical, gromacs, pymol, rasmol, r-other-bio3d, massxpert
+Why: Molecular modelling and molecular dynamics.
+Comment: r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team
+
+Depends: plasmidomics
+Why: Presentation
+
+X-Begin-Category: Tools for the molecular biologist.
+
+Depends: biosquid, gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
+
+Depends: melting
+Published-Authors: Nicolas Le Novère
+Published-Title: MELTING, computing the melting temperature of nucleic acid duplex
+Published-In: Bioinformatics, 17: S.1226-1227
+Published-Year: 2001
+
+Depends: mipe
+Published-Authors: Aerts J & Veenendaal T.
+Published-Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
+Published-In: Online Journal of Bioinformatics 6(2): 114-120
+Published-Year: 2005
+
+Depends: primer3
+Published-Authors: S. Rozen, H. Skaletsky
+Published-Title: Primer3 on the WWW for general users and for biologist programmers
+Published-In: Methods Mol Biol. 132:365-86
+Published-Year: 2000
+
+X-End-Category: Tools for the molecular biologist.
+
+Suggests: mozilla-biofox
+Why: Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
+
+Depends: glam2
+Why: Motif search
+
+Depends: sequenceconverter.app
+
+Depends: raster3d
+
+Depends: phyml
+
+Depends: autodock
+Enhanced-By: autogrid
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Why: Molecular modelling and molecular dynamics.
+
+
+Depends: autodocktools
+Enhanced-By: mgltools-dejavu, mgltools-pmv, mgltools-utpackages, mgltools-vision, mgltools-volume, mgltools-bhtree, mgltools-geomutils, mgltools-opengltk, mgltools-pyglf, mgltools-sff, pdb2pqr
+Comment: The package autodocktools depends from the mgltools-* packages mentioned
+ above, so they will be installed even if they would not be mentioned in
+ the list of Depends in the metapackage med-bio. But leaving them out here
+ would hide them from the tasks and bugs list as well from the sectioning in
+ http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3
+ so they are mentioned here in addition to autodocktools.
+
+Depends: mustang
+Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
+Published-Title: MUSTANG: A multiple structural alignment algorithm
+Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
+Published-Year: 2006
+
+Depends: theseus
+
+Depends: staden-io-lib-utils
+
+Depends: r-other-genabel
+Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
+Responsible: Steffen Moeller <steffen_moeller at gmx.de>
+License: GPL 2+
+WNPP: 492044
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-genabel/trunk/
+Pkg-Description: genome-wide SNP association analysis
+ A package for genome-wide association analysis between quantitative
+ or binary traits and single-nucleiotide polymorphisms (SNPs).
+
+Depends: meme
+Homepage: http://meme.nbcr.net/meme/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/meme/trunk/
+Pkg-Description: motif discovery and search
+ MEME is a tool for discovering motifs in a group of related DNA or protein
+ sequences. A motif is a sequence pattern that occurs repeatedly in a group
+ of related protein or DNA sequences. MEME represents motifs as position-dependent
+ letter-probability matrices which describe the probability of each possible
+ letter at each position in the pattern. Individual MEME motifs do not contain
+ gaps. Patterns with variable-length gaps are split by MEME into two or more
+ separate motifs.
+ .
+ MEME takes as input a group of DNA or protein sequences (the training set)
+ and outputs as many motifs as requested. MEME uses statistical modeling
+ techniques to automatically choose the best width, number of occurrences,
+ and description for each motif.
+
+Depends: vienna-rna
+Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: non-free but redistributable
+WNPP: 451193
+Pkg-Description: RNA sequence analysis
+ The Vienna RNA Package consists of a C code library and several
+ stand-alone programs for the prediction and comparison of RNA secondary
+ structures.
+
+Depends: cytoscape
+Homepage: http://cytoscape.org/
+Responsible: Mike Smoot <mes at aescon.com>
+License: LGPL
+WNPP: 465331
+Pkg-Description: visualizing molecular interaction networks
+ Cytoscape is a bioinformatics software platform for visualizing molecular
+ interaction networks and integrating these interactions with gene expression
+ profiles and other state data. Additional features are available as plugins.
+
+Depends: ballview
+
+Depends: raxml
+Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
+License: GPL
+Pkg-Description: Randomized Axelerated Maximum Likelihood
+ RAxML is a program for sequential and parallel Maximum Likelihood-based
+ inference of large phylogenetic trees. It has originally been derived
+ from fastDNAml.
+ .
+ There are freely accessible web-servers available for RAxML at
+ http://phylobench.vital-it.ch/raxml-bb/ and
+ http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .
+
+Depends: axparafit
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL
+WNPP: 464323
+Pkg-Description: optimized statistical analysis of host-parasite coevolution
+ AxParafit is a highly optimized version of Pierre Legendre's Parafit
+ program for statistical analysis of host-parasite coevolution.
+ AxParafit has been parallelized with MPI (Message Passing Interface)
+ for compute clusters and was used to carry out the largest
+ co-evolutionary analysis to date for the paper describing the software.
+
+Depends: axpcoords
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL
+WNPP: 464323
+Pkg-Description: LAPACK-based implementation of DistPCoA
+ AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
+ http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
+ which is another program by Pierre Legendre, it conducts a principal
+ coordinates analysis.
+ This program is required for the pipeline that conducts a full host-parasite
+ co-phylogenetic analysis in combination with AxParafit.
+
+Depends: copycat
+Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
+License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
+Pkg-Description: fast access to cophylogenetic analyses
+ CopyCat provides an easy and fast access to cophylogenetic analyses.
+ It incorporates a wrapper for the program ParaFit, which conducts a
+ statistical test for the presence of congruence between host and
+ parasite phylogenies. CopyCat offers various features, such as the
+ creation of customized host-parasite association data and the
+ computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
+
+Depends: btk-core
+Homepage: http://sourceforge.net/projects/btk/
+Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
+License: GPL
+WNPP: 459753
+Pkg-Description: biomolecule Toolkit C++ library
+ The Biomolecule Toolkit is a library for modeling biological
+ macromolecules such as proteins, DNA and RNA. It provides a C++ interface
+ for common tasks in structural biology to facilitate the development of
+ molecular modeling, design and analysis tools.
+
+Depends: tacg
+Homepage: http://sourceforge.net/projects/tacg
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL and others
+WNPP: 461504
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/tacg/trunk/
+Pkg-Description: command line program for finding patterns in nucleic acids
+ tacg is a character-based, command line tool for unix-like operating systems
+ for pattern-matching in nucleic acids and performing some of the basic protein
+ manipulations. It was originally designed for restriction enzyme analysis of
+ DNA, but has been extended to other types of matching. It now handles
+ degenerate sequence input in a variety of matching approaches, as well as
+ patterns with errors, regular expressions and TRANSFAC-formatted matrices.
+ .
+ It was designed to be a grep for DNA and like the original grep, its
+ capabilities have grown so that now the author has to keep calling up the help
+ page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
+ application in any sense. However, it's existance as a strictly command-line
+ tool lends itself well to Webification and wrapping by various GUI tools and
+ it is now distributed with a web interface form and a Perl CGI handler.
+ Additionally, it can easily be integrated into editors that support shell
+ commands such as nedit.
+ .
+ The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
+ BMC Bioinformatics. 3:8 http://www.biomedcentral.com/1471-2105/3/8
+
+Depends: treeplot
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL
+WNPP: 461508
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot
+Pkg-Description: Phylogenetic tree file converter
+ Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
+ Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
+ (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
+ (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
+ file (.pnm)
+ .
+ The upstream author Olivier Langella says: 'I think that "treeplot"
+ is outdated. "Treeviewx" is an equivalent that works great and it is
+ already packaged. ... you can replace "treeplot" with
+ "populations". I would be pleased if "populations" became a Debian
+ package.' So this package should probably be delisted in favour of
+ populations (see http://lists.debian.org/debian-med/2008/03/msg00124.html).
+
+Depends: treevolve
+Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
+Responsible: Charles Plessy <plessy at debian.org>
+License: has to be verified
+WNPP: 461510
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve
+Pkg-Description: simulation of evolution of DNA sequences
+ treevolve will simulate the evolution of DNA sequences under a
+ coalescent model, which allows exponential population growth,
+ population subdivision according to an island model, migration and
+ recombination. In addition different periods of population dynamics
+ can be enforced at different times. For example, a period of
+ exponential growth can be followed by a period of stasis where the
+ population is subdivided into demes. Multiple sets of such simulated
+ sequence data can then be compared to sequence data sampled from a
+ population of interest using suitable statistics, and various
+ evolutionary hypotheses concerning the evolution of this population
+ tested.
+ .
+ Citation: Population dynamics of HIV-1 inferred from gene sequences
+ Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
+
+Depends: asap
+Homepage: http://asap.ahabs.wisc.edu/software/asap/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Pkg-Description: organize the data associated with a genome
+ Developments in genome-wide approaches to biological research have
+ yielded greatly increased quantities of data, necessitating the cooperation
+ of communities of scientists focusing on shared sets of data. ASAP
+ leverages the internet and database technologies to meet these needs.
+ ASAP is designed to organize the data associated with a genome from the
+ early stages of sequence annotation through genetic and biochemical
+ characterization, providing a vehicle for ongoing updates of the annotation
+ and a repository for genome-scale experimental data. Development was
+ motivated by the need to more directly involve a greater community of
+ researchers, with their collective expertise, in keeping the genome
+ annotation current and to provide a synergistic link between up-to-date
+ annotation and functional genomic data. The system is continually under
+ development at the Genome Evolution Lab with the stable, in-use, publicly
+ available University of Wisconsin installation updated regularly.
+ .
+ Software development on ASAP began in early 2002, and ASAP has been
+ continually improved up until the present day. A longstanding goal of
+ the ASAP project was to make the source code of ASAP available so that
+ other installations of ASAP could be implemented. As future ASAP
+ installations come to pass, ASAP will be further extended to be
+ inter-operable between sites.
+
+Depends: emboss-kaptain
+Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL-2+
+WNPP: 466682
+Pkg-Description: graphical interface to EMBOSS using Kaptain
+ EMBOSS.kaptn is a graphical user interface (GUI) for more than 200
+ programms of the EMBOSS sequence analysis package. It uses Kaptain, a
+ universal front-end for command line applications. EMBOSS is a
+ collection of high-quality free Open Source software for sequence
+ analysis. With EMBOSS.kaptn it integrates nicely into X window based
+ desktops like KDE.
+
+Depends: agdbnet
+Homepage: http://pubmlst.org/software/database/agdbnet/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+WNPP: 500106
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/agdbnet/trunk/
+Pkg-Description: antigen sequence database software for web-based bacterial typing
+ AgdbNet is antigen sequence database software for web-based bacterial
+ typing. The software facilitates simultaneous BLAST querying of multiple
+ loci using either nucleotide or peptide sequences. It's written in Perl
+ and runs on Linux/UNIX systems.
+ .
+ Databases are described by XML files and can have any number of loci, which
+ may be defined by nucleotide and/or peptide sequences. The databases can
+ optionally have integral isolate tables so that information about representative
+ isolates can be retrieved or they may be configured to query external isolate
+ databases, such as those hosted on PubMLST.org.
+ .
+ The software is used on a number of public bacterial typing databases:
+ * Neisseria PorA variable regions | PorB | FetA
+ * Campylobacter flaA
+ * Streptococcus equi seM
+
+Depends: martj
+Homepage: http://www.ebi.ac.uk/biomart/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/martj/trunk/
+Pkg-Description: distributed data integration system for biological data
+ BioMart is a simple, distributed data integration system with
+ powerful query capabilities. The BioMart data model has been applied
+ to the following data sources: UniProt Proteomes, Macromolecular
+ Structure Database (MSD), Ensembl, Vega, and dbSNP.
+
+Depends: cluster3
+Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
+License: non-free
+WNPP: 286167
+Responsible: Steffen Moeller <moeller at debian.org>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/cluster3/trunk/
+Pkg-Description: find clustering solutions for genome data
+ Cluster 3.0 is an enhanced version of Cluster, which was originally
+ developed by Michael Eisen while at Stanford University. The main
+ improvement consists of the k-means algorithm, which now includes
+ multiple trials to find the best clustering solution. This is crucial
+ for the k-means algorithm to be reliable. The routine for self-organizing
+ maps was extended to include 2D rectangular geometries. The Euclidean
+ distance and the city-block distance were added to the available
+ measures of similarity.
+
+Depends: jmol
+Homepage: http://jmol.sourceforge.net/
+Responsible: Vincent Fourmond <fourmond at debian.org>
+License: LGPL
+WNPP: 512930
+Vcs-Svn: svn://svn.debian.org/svn/pkg-escience/jmol/trunk/debian/
+Pkg-Description: viewer for chemical structures in 3D
+ Jmol is a Java molecular viewer for three-dimensional chemical structures.
+ Features include reading a variety of file types and output from quantum
+ chemistry programs, and animation of multi-frame files and computed normal
+ modes from quantum programs. It includes with features for chemicals,
+ crystals, materials and biomolecules.
+ * The JmolApplet is a web browser applet that can be integrated into
+ web pages.
+ * The Jmol application is a standalone Java application that runs on
+ the desktop.
+ * The JmolViewer is a development tool kit that can be integrated into
+ other Java applications.
+X-Comment:
+ For more detailed information about packaging status please see
+ http://lists.debian.org/debian-med/2008/03/msg00097.html before
+ you might download the source packages http://debian.wgdd.de/temp/jmol/
+
+Depends: jtreeview
+Homepage: http://jtreeview.sourceforge.net/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+WNPP: 243771
+X-Category: Visualisation
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treeview/trunk/
+Pkg-Description: Java re-implementation of Michael Eisen's TreeView
+ TreeView creates a matrix-like display of expression data, known as
+ Eisen clustering. The original implementation was a Windows program
+ named TreeView by Michael Eisen. This TreeView package, sometimes also
+ referred to as jTreeView, was rewritten in Java under a free license,
+ the original implementation also comes with the source code, but controls
+ commercial distribution. And it did not run on Unix.
+ .
+ Java TreeView is an extensible viewer for microarray data in
+ PCL or CDT format.
+
+Depends: smile
+Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 221492
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/smile/trunk/
+Pkg-Description: infer motifs in a set of sequences
+ SMILE is a tool that infers motifs in a set of sequences, according to some
+ criteria. It was first made to infer exceptional sites as binding sites in
+ DNA sequences. Since the 1.4 version, it allows to infer motifs written on
+ any alphabet (even degenerate) in any kind of sequences.
+ .
+ The specificity of SMILE is to allow to deal with what we call structured
+ motifs, which are motifs associated by some distance constraints.
+
+Depends: cactus
+Homepage: http://www.cactuscode.org/Community/Biology.html
+License: GPL
+Pkg-Description:
+ Cactus is an open source problem solving environment designed for scientists
+ and engineers. Its modular structure easily enables parallel computation
+ across different architectures and collaborative code development between
+ different groups.
+ .
+ Cactus provides easy access to many cutting edge software technologies being
+ developed in the academic research community, including the Globus
+ Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
+ adaptive mesh refinement, web interfaces, and advanced visualization tools.
+
+Depends: contralign
+Homepage: http://contra.stanford.edu/contralign/
+License: Public Domain
+Pkg-Description: parameter learning framework for protein pairwise sequence alignment
+ CONTRAlign is an extensible and fully automatic parameter learning
+ framework for protein pairwise sequence alignment based on pair
+ conditional random fields. The CONTRAlign framework enables the
+ development of feature-rich alignment models which generalize well to
+ previously unseen sequences and avoid overfitting by controlling model
+ complexity through regularization.
+
+Depends: galaxy
+Homepage: http://g2.trac.bx.psu.edu/
+License: MIT
+WNPP: 432472
+Pkg-Description: manipulate sequences and annotation files
+ Galaxy is a web-based tool allowing users to perform operations which
+ are usually done with command-line interface. Using galaxy, one can
+ manipulate sequences and annotation files in many formats. Galaxy has
+ strong ties with the UCSC genome browser, and makes it easy to
+ visualise modified annotation files as a custom track.
+
+Depends: genographer
+Homepage: http://hordeum.oscs.montana.edu/genographer/
+License: GPL
+Pkg-Description: read data and reconstruct them into a gel image
+ This program will read in data from an ABI 3700, 3100, 377 or 373,
+ CEQ 2000 or SCF and reconstruct them into a gel image which is
+ straightened and sized. Bins can be defined easily and viewed as
+ thumbnails, which allows for a fairly quick and easy way of scoring a gel.
+ .
+ The program is written in Java and uses the Java 1.3 API. Therefore,
+ it should run on any machine that can run java.
+
+Depends: molekel
+Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
+License: GPL
+Pkg-Description: multiplatform molecular visualization
+ Molekel is an opensource (GPL) multiplatform molecular visualization
+ program being developed at the Swiss National Supercomputing Centre
+ (CSCS).
+
+Depends: pftools
+Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
+License: GPL
+Pkg-Description: tools to handle patterns from PROSITE
+ ps_scan is a perl program used to scan one or several patterns, rules
+ and/or profiles from PROSITE against one or several protein sequences
+ in Swiss-Prot or FASTA format. It requires two compiled external
+ programs from the PFTOOLS, which are also distributed with the sources.
+
+Depends: proalign
+Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
+License: GPL
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 378290
+Pkg-Description: Probabilistic multiple alignment program
+ ProAlign performs probabilistic sequence alignments using hidden Markov
+ models (HMM). It includes a graphical interface (GUI) allowing to (i)
+ perform alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions and
+ (iv) export alignments to other softwares.
+ .
+ ProAlign uses a progressive method, such that multiple alignment is
+ created stepwise by performing pairwise alignments in the nodes of a
+ guide tree. Sequences are described with vectors of character
+ probabilities, and each pairwise alignment reconstructs the ancestral
+ (parent) sequence by computing the probabilities of different
+ characters according to an evolutionary model. It has been published in
+ Bioinformatics. 2003 Aug 12;19(12):1505-13.
+
+Depends: ssaha
+Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
+License: GPL
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 425111
+Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
+ SSAHA is a software tool for very fast matching and alignment of DNA
+ sequences. It achieves its fast search speed by converting sequence
+ information into a `hash table' data structure, which can then be
+ searched very rapidly for matches. It was published by Ning Z,
+ Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
+ .
+ SSAHA is the only free software of its category (fast search of nearly
+ indentical sequences). The popular alternative, BLAT, is restricted to
+ non-commercial use.
+ .
+ Unfortunately the source of its successor ssaha2
+ http://www.sanger.ac.uk/Software/analysis/SSAHA2/
+ does not seem to be available.
+
+Depends: ngila
+Homepage: http://scit.us/projects/ngila/
+License: GPLv3
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 439996
+Pkg-Description: global pairwise alignments with logarithmic and affine gap costs
+ Ngila is an application that will find the best alignment of a pair
+ of sequences using log-affine gap costs, which are the most
+ biologically realistic gap costs.
+ .
+ Ngila implements the Miller and Myers (1988) algorithm in order to
+ find a least costly global alignment of two sequences given homology
+ costs and a gap cost. Two versions of the algorithm are
+ included: holistic and divide-and-conquer. The former is faster but
+ the latter utilizes less memory. Ngila starts with the
+ divide-and-conquer method but switches to the holistic method for
+ subsequences smaller than a user-established threshold. This improves
+ its speed without substantially increasing memory requirements. Ngila
+ also allows users to assign costs to end gaps that are smaller than
+ costs for internal gaps. This is important for aligning using the
+ free-end-gap method.
+ .
+ Ngila is published in Cartwright RA Bioinformatics 2007
+ 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
+
+Depends: tm-align
+Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
+License: free to change and redistribute
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 447505
+Pkg-Description: structural protein alignment
+ TM-align is a structural alignment program for comparing two proteins
+ whose sequences can be different. TM-align will first find the best
+ equivalent residues of two proteins based on the structure similarity
+ and then output a TM-score.
+ .
+ TM-align performs a structural alignment of protein sequences. It is
+ said to be 10 times faster than DALI and no worse in accuracy.
+
+Depends: dazzle
+Homepage: http://www.biojava.org/dazzle
+Responsible: Steffen Moeller <moeller at debian.org>
+License: LGPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dazzle/trunk/
+Pkg-Description: Java-based DAS server
+ Dazzle is a general purpose server for the Distributed Annotation System
+ (DAS) protocol. It is implemented as a Java servlet, using the BioJava
+ APIs. Dazzle is a modular system which uses small "datasource" plugins to
+ provide access to a range of databases. Several general-purpose plugins
+ are included in the package, and it it straightforward to develop new
+ plugins to connect to your own databases.
+ .
+ Information on DAS is available from http://www.biodas.org/
+
+Depends: ecell
+Homepage: http://www.e-cell.org/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 241195
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ecell/trunk/
+Pkg-Description: Concept and environment for constructing virtual cells on computers
+ The E-Cell Project is an international research project aiming at
+ developing necessary theoretical supports, technologies and software
+ platforms to allow precise whole cell simulation.
+ .
+ The E-Cell System is an object-oriented software suite for modeling,
+ simulation, and analysis of large scale complex systems such as
+ biological cells, architected by Kouichi Takahashi and written by
+ a team of developers.
+ .
+ The core part of the system, E-Cell Simulation Environment version 3,
+ allows many components driven by multiple algorithms with different
+ timescales to coexist.
+ .
+ E-Cell System consists of the following three major parts:
+ * E-Cell Simulation Environment (or E-Cell SE)
+ * E-Cell Modeling Environment (or E-Cell ME)
+ * E-Cell Analysis Toolkit.
+
+Depends: ncoils
+Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 299856
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ciols/trunk/
+Pkg-Description: coiled coil secondary structure prediction
+ The program predicts the coiled coil secondary structure predictions
+ from protein sequences. The algorithm was published in
+ Lupas, van Dyke & Stock, Predicting coiled coils from
+ protein sequences Science, 252, 1162-1164, 1991.
+
+Depends: haploview
+Homepage: http://www.broad.mit.edu/mpg/haploview/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 311421
+License: DFSG free
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/haploview/trunk/
+Pkg-Description: Analysis and visualization of LD and haplotype maps
+ This tools assists in the analysis of the nucleotide
+ variation in a population. Such investigations are performed
+ to determine genes and genetic pathways that are associated
+ with diseases. This is an early stage in the quest for new drugs.
+
+Depends: bio-mauve
+Homepage: http://asap.ahabs.wisc.edu/mauve/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Language: C++ and Java
+X-Category: Multiple genome alignment
+X-Importance: efficient
+Pkg-Description: multiple genome alignment
+ Mauve is a system for efficiently constructing multiple genome alignments
+ in the presence of large-scale evolutionary events such as rearrangement
+ and inversion. Multiple genome alignment provides a basis for research
+ into comparative genomics and the study of evolutionary dynamics. Aligning
+ whole genomes is a fundamentally different problem than aligning short
+ sequences.
+ .
+ Mauve has been developed with the idea that a multiple genome aligner
+ should require only modest computational resources. It employs algorithmic
+ techniques that scale well in the amount of sequence being aligned. For
+ example, a pair of Y. pestis genomes can be aligned in under a minute,
+ while a group of 9 divergent Enterobacterial genomes can be aligned in
+ a few hours.
+ .
+ Mauve computes and interactively visualizes genome sequence comparisons.
+ Using FastA or GenBank sequence data, Mauve constructs multiple genome
+ alignments that identify large-scale rearrangement, gene gain, gene loss,
+ indels, and nucleotide substutition.
+ .
+ Mauve is developed at the University of Wisconsin.
+ .
+ Note: There are instructions for compiling Mauve from source available at
+ http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html
+
+Depends: mauvealigner
+Homepage: http://asap.ahabs.wisc.edu/mauve/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mauvealign/trunk/
+Pkg-Description: multiple genome alignment algorithms
+ The mauveAligner and progressiveMauve alignment algorithms have been
+ implemented as command-line programs included with the downloadable Mauve
+ software. When run from the command-line, these programs provide options
+ not yet available in the graphical interface.
+ .
+ Mauve is a system for efficiently constructing multiple genome alignments
+ in the presence of large-scale evolutionary events such as rearrangement
+ and inversion. Multiple genome alignment provides a basis for research
+ into comparative genomics and the study of evolutionary dynamics. Aligning
+ whole genomes is a fundamentally different problem than aligning short
+ sequences.
+ .
+ Mauve has been developed with the idea that a multiple genome aligner
+ should require only modest computational resources. It employs algorithmic
+ techniques that scale well in the amount of sequence being aligned. For
+ example, a pair of Y. pestis genomes can be aligned in under a minute,
+ while a group of 9 divergent Enterobacterial genomes can be aligned in
+ a few hours.
+ .
+ Mauve computes and interactively visualizes genome sequence comparisons.
+ Using FastA or GenBank sequence data, Mauve constructs multiple genome
+ alignments that identify large-scale rearrangement, gene gain, gene loss,
+ indels, and nucleotide substutition.
+ .
+ Mauve is developed at the University of Wisconsin.
+
+Depends: gbrowse
+Homepage: http://www.gmod.org/wiki/index.php/GBrowse
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 429610
+License: Perl Artistic License, plus additional clauses
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse
+X-Category: Genome Browser
+X-Importance: Academic ones are really expensive for commercial use
+Pkg-Description: The Generic Genome Browser from GMOD
+ The Generic Genome Browser is a combination of database and interactive Web
+ page for manipulating and displaying annotations on genomes. Some of its
+ features:
+ * Simultaneous bird's eye and detailed views of the genome.
+ * Scroll, zoom, center.
+ * Attach arbitrary URLs to any annotation.
+ * Order and appearance of tracks are customizable by administrator and end-user.
+ * Search by annotation ID, name, or comment.
+ * Supports third party annotation using GFF formats.
+ * Settings persist across sessions.
+ * DNA and GFF dumps.
+ * Connectivity to different databases, including BioSQL and Chado.
+ * Multi-language support.
+ * Third-party feature loading.
+ * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
+ find oligonucleotides, design primers, create restriction maps, edit features)
+
+Depends: mira
+Homepage: http://chevreux.org/projects_mira.html
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 435915
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
+Pkg-Description: Whole Genome Shotgun and EST Sequence Assembler
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+ specialised on reconstructing pristine mRNA transcripts while
+ detecting and classifying single nucleotide polymorphisms (SNP)
+ occuring in different variations thereof.
+ .
+ The assembler is routinely used for such various tasks as mutation
+ detection in different cell types, similarity analysis of transcripts
+ between organisms, and pristine assembly of sequences from various
+ sources for oligo design in clinical microarray experiments.
+
+Depends: phylographer
+Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 426489
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phylographer/trunk/
+Pkg-Description: Graph Visualization Tool
+ PhyloGrapher is a program designed to visualize and study evolutionary
+ relationships within families of homologous genes or proteins
+ (elements). PhyloGrapher is a drawing tool that generates custom graphs
+ for a given set of elements. In general, it is possible to use
+ PhyloGrapher to visualize any type of relations between elements.
+ Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
+ the results of a BLAST search as a graph.
+ .
+ PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
+ biological sequence alignment reports (BLAST is provided by Debian's
+ blast2 package).
+
+Depends: phylowin
+Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 395840
+License: unknown
+Pkg-Description: Graphical interface for molecular phylogenetic inference
+ Phylo_win is a graphical colour interface for molecular phylogenetic
+ inference. It performs neighbor-joining, parsimony and maximum
+ likelihood methods and bootstrap with any of them. Many distances can be
+ used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
+ (1995), LogDet for nucleotidic sequences, Poisson correction for protein
+ sequences, Ka and Ks for codon sequences. Species and sites to include
+ in the analysis are selected by mouse. Reconstructed trees can be drawn,
+ edited, printed, stored and evaluated according to numerous criteria.
+ .
+ This program uses sources files from the Phylip program, which forbids
+ its use for profit. Therfore, Phylo_win will unfortunately have to be
+ distributed in contrib or non-free.
+
+Depends: seq-gen
+Homepage: http://tree.bio.ed.ac.uk/software/seqgen/
+License: Free
+Pkg-Description: simulate the evolution of nucleotide or amino acid sequences
+ Seq-Gen is a program that will simulate the evolution of nucleotide or
+ amino acid sequences along a phylogeny, using common models of the
+ substitution process. A range of models of molecular evolution are
+ implemented including the general reversible model. State frequencies
+ and other parameters of the model may be given and site-specific rate
+ heterogeneity may also be incorporated in a number of ways. Any number
+ of trees may be read in and the program will produce any number of data
+ sets for each tree. Thus large sets of replicate simulations can be easily
+ created. It has been designed to be a general purpose simulator that
+ incorporates most of the commonly used (and computationally tractable)
+ models of molecular sequence evolution.
+
+Depends: wgs-assembler
+Homepage: http://wgs-assembler.sourceforge.net/
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 395843
+License: GPL
+Pkg-Description: Whole-Genome Shotgun Assembler
+ Celera Assembler is scientific software for DNA research. It can
+ reconstruct long sequences of genomic DNA given the fragmentary data
+ produced by whole-genome shotgun sequencing. The Celera Assembler
+ enabled many advances in genomics, including the first genome
+ sequence of a multi-cellular organism and the first diploid sequence
+ of an individual human.
+ .
+ The Celera Assembler is a member of a class of software called
+ whole-genome shotgun assemblers. The Celera Assembler is mature,
+ efficient, open-source software with a long record of contributions
+ to science. Celera Assembler is written mostly in C for unix
+ operating systems. Although it requires large compute resources to
+ resolve complex genomes, it can assemble bacterial genomes on a
+ laptop.
+ .
+ This important software is an "open source" project. Originally
+ developed at Celera Genomics, it was released under the GNU Public
+ License and deposited on a public repository (Source Forge) in
+ 2004. Scientists around the world can download, build, and run the
+ software without restriction. In addition, they can inspect the
+ source code and alter it at their own sites. Workers at JCVI and a
+ few other institutes regularly submit their code alterations to the
+ public repository.
+ .
+ JCVI has made many important contributions to Celera
+ Assembler. Scientists and engineers at JCVI are extending the code to
+ handle more and more polymorphic data sets, including environmental
+ samples. In collaboration with scientists at the University of
+ Maryland, they are adding the capability to assemble pyrosequencing
+ data (as from a 454 FLX machine) in addition to the traditional
+ Sanger sequencing data (as from an ABI 3730 machine). JCVI's efforts
+ provide the cutting edge software that genome scientists around the
+ world will need as they apply DNA sequencing technology to more and
+ more difficult problems of biology.
+ .
+ See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: gbioseq
+Homepage: http://www.bioinformatics.org/project/?group_id=94
+License: GPL
+Pkg-Description: DNA sequence editor for Linux
+ gBioSeq is in an early stage of development, but it is already running.
+ The goal is to provide an easy to use software to edit DNA sequences under
+ Linux, Windows, MacOsX, using GTK C# (Mono).
+
+Depends: populations
+Homepage: http://bioinformatics.org/~tryphon/populations/
+License: GPL
+Pkg-Description: individuals or populations distances based on allelic frequencies
+ Population genetic software (individuals or populations distances, phylogenetic trees)
+ * haploids, diploids or polyploids genotypes (see input formats)
+ * structured populations (see input files structured populations
+ * No limit of populations, loci, alleles per loci (see input formats)
+ * Distances between individuals (15 different methods)
+ * Distances between populations (15 methods)
+ * Bootstraps on loci OR individuals
+ * Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA
+ (PHYLIP tree format)
+ * Allelic diversity
+ * Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
+ Populations...)
+
+Depends: phpphylotree
+Homepage: http://www.bioinformatics.org/project/?group_id=372
+License: GPL
+Pkg-Description: draw phylogenetic trees
+ PhpPhylotree is a web application that is able to draw phylogenetic trees.
+ It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
+
+Depends: tracetuner
+Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
+License: GPL; but US Patent #6,681,186
+Pkg-Description: DNA sequencing and trace processing
+ TraceTuner is a DNA sequencing quality value, base calling and trace
+ processing software application originally developed by Paracel,
+ Inc. While providing a flexible interface and capability to adopt the
+ "pure" base calls produced by Phred, KB or any other "original"
+ caller, it offers competitive features not currently available in
+ other tools, such as customized calibration of quality values,
+ advanced heterozygote and mixed base calling and deconvolving the
+ "mixed" electropherograms resulting from the presence of indels into
+ a couple of "pure" electropherograms. Previous versions of TraceTuner
+ were used by Celera Genomics to process over 27 million reads from
+ both Drosophila and human genome projects and by Applied Biosystems,
+ as a component of its SNP detection and genotyping software product
+ SeqScape. TraceTuner implements an advanced peak processing
+ technology for resolving overlapping peaks of the same dye color into
+ individual, or "intrinsic" peaks. This technology was protected by US
+ Patent #6,681,186. Currently, TraceTuner is an open source software,
+ which has been used by J. Craig Venter Institute's DNA Sequencing and
+ Resequencing pipelines.
+ .
+ The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All
+ rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is
+ being made available free of charge by Applera Corporation subject to the terms
+ and conditions of the GNU General Public License, version 2, as published by the
+ Free Software Foundation (the "GNU General Public License").
+
+Depends: twain
+Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
+License: Open Source
+Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
+ TWAIN is a new syntenic genefinder which employs a Generalized Pair
+ Hidden Markov Model (GPHMM) to predict genes in two closely related
+ eukaryotic genomes simultaneously. It utilizes the MUMmer package to
+ perform approximate alignment before applying a GPHMM based on an
+ enhanced version of the TigrScan gene finder. TWAIN was written by
+ Bill Majoros and Mihaela Pertea while at The Institute for Genomic
+ Research (TIGR).
+ .
+ TWAIN consists of two components: (1) ROSE, the Region Of Synteny
+ Extractor, which identifies contiguous regions likely to contain one
+ or more syntenic genes, and (2) OASIS, a generalized pair hidden
+ Markov model (GPHMM) for predicting genes in the regions identified
+ by ROSE. The system utilizes approximate alignments constructed by
+ the PROmer and NUCmer programs in the MUMmer package to assess
+ approximate alignment scores efficiently. More detailed information
+ on the architecture of this system will be made available soon.
+ Slides from a talk at Computational Genomics 2004 are now available.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: rose
+Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
+License: Open Source
+Pkg-Description: Region-Of-Synteny Extractor
+ ROSE is a program which identifies regions between two genomes which
+ are likely to contain orthologous genes. The two genomes are given as
+ two multi fasta files of DNA sequences. The PROmer program from the
+ MUMmer package needs to be run first between the two genomes, and the
+ resulting delta file is then input to ROSE. If a previous annotation
+ is available for one or both genomes, then the coordinates of the
+ annotated genes from a genome can be optionally given as input in a
+ gff file. The gene coordinates will be used to guide the length of
+ the regions produced by ROSE. By default, when finding a region of
+ consistent alignments, ROSE will add a user-defined margin (1000 bp
+ by default) on either side of that region. When a predicted gene
+ overlaps an alignment we use the gene prediction to extend the
+ boundaries of the output region.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: glimmerhmm
+Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
+License: Artistic
+Pkg-Description: Eukaryotic Gene-Finding System
+ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
+ Model (GHMM). Although the gene finder conforms to the overall
+ mathematical framework of a GHMM, additionally it incorporates splice
+ site models adapted from the GeneSplicer program and a decision tree
+ adapted from GlimmerM. It also utilizes Interpolated Markov Models
+ for the coding and noncoding models . Currently, GlimmerHMM's GHMM
+ structure includes introns of each phase, intergenic regions, and
+ four types of exons (initial, internal, final, and single). A basic
+ user manual can be consulted here.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: genezilla
+Homepage: http://www.genezilla.org/
+License: Artistic
+Pkg-Description: eukaryotic gene finder
+ GeneZilla is a state-of-the-art program for computational prediction
+ of protein-coding genes in eukaryotic DNA, and is based on the
+ Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
+ and GENIE. It is highly reconfigurable and includes software for
+ retraining by the end-user. It is written in highly optimized C++ and
+ runs under most UNIX/Linux platforms. The run time and memory
+ requirements are linear in the sequence length, and are in general
+ much better than those of competing systems, due to GeneZilla's novel
+ decoding algorithm. Graph-theoretic representations of the high
+ scoring open reading frames are provided, allowing for exploration of
+ sub-optimal gene models. It utilizes Interpolated Markov Models
+ (IMMs), Maximal Dependence Decomposition (MDD), and includes states
+ for signal peptides, branch points, TATA boxes, CAP sites, and will
+ soon model CpG islands as well.
+ .
+ GeneZilla is an open-source project hosted at bioinformatics.org and
+ currently consists of ~20,000 lines of code. GeneZilla evolved out
+ of the ab initio eukaryotic gene finder TIGRscan, which was developed
+ at The Institute for Genomic Research over a 3-year period under NIH
+ grants R01-LM06845 and R01-LM007938, and which served as the basis
+ for the comparative gene finder TWAIN.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: exalt
+Homepage: http://www.cbcb.umd.edu/software/exalt/
+License: Artistic
+Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
+ ExAlt is a software program designed to predict alternatively spliced
+ overlapping exons in genomic sequence. The program works in several
+ ways depending on the available input. ExAlt can use information of
+ existing gene structure as well as sequence conservation to improve
+ the precision of it's predictions. ExAlt can also make predictions
+ when only a single genomic sequence is available. ExAlt has been
+ extensively tested on Drosophila melanogaster, but can be adapted to
+ run on other species.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: jigsaw
+Homepage: http://www.cbcb.umd.edu/software/jigsaw/
+License: Artistic
+Pkg-Description: gene prediction using multiple sources of evidence
+ JIGSAW is a program designed to use the output from gene finders,
+ splice site prediction programs and sequence alignments to predict
+ gene models. The program provides an automated way to take advantage
+ of the many succsessful methods for computational gene prediction and
+ can provide substantial improvements in accuracy over an individual
+ gene prediction program.
+ .
+ JIGSAW is available for all species. It is tested on Human, Rice
+ (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
+ neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
+ fumigatus, Plasmodium falciparum and Plasmodium yoelii.
+ .
+ The linear combiner option is now available in the current JIGSAW
+ software distribution. This allows JIGSAW to be run without the use
+ of training data. A weight is assigned to each evidence source, and
+ gene predictions are based on a weighted voting scheme, yielding the
+ best 'consensus' predictions.
+ .
+ Predictions are now available for the ENCODE regions in Human and
+ viewable as custom tracks in the UCSC Human Genome
+ Browser. Predictions available for the Human genome and viewable as
+ custom tracks in the UCSC Human Genome Browser
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: genesplicer
+Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
+License: Artistic
+Pkg-Description: computational method for splice site prediction
+ A fast, flexible system for detecting splice sites in the genomic DNA
+ of various eukaryotes. The system has been trained and tested
+ successfully on Plasmodium falciparum (malaria), Arabidopsis
+ thaliana, human, Drosophila, and rice . Training data sets for human
+ and Arabidopsis thaliana are included. Use the GeneSplicer Web
+ Interface to run GeneSplicer directly, or see below for instructions
+ on downloading the complete system including source code.
+ .
+ There is no independent program to train GeneSplicer, but there is a
+ way to obtain the necessary files by using the training procedure of
+ GlimmerHMM.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Ignore: riso
+Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
+License: not specified
+Pkg-Description: motif discovery tool
+ RISO discovers motifs composed of many binding sites separated by
+ spacers. Each binding site is called a box
+ .
+ The author of SMILE claims at his homepage
+ http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
+ faster and more powerfull than SMILE which is described itself as
+ "SMILE is a tool that infers motifs in a set of sequences, according
+ to some criterias. It was first made to infer exceptionnal sites as
+ binding sites in DNA sequences. It allows to infer motifs written on
+ any alphabet (even degenerate) in any kind of sequences. The
+ specificity of SMILE is to allow to deal with what we call
+ "structured motifs", which are motifs associated by some distance
+ constraints. In particular, SMILE is able to group under a unique
+ model different occurrences composed of several boxes separated by
+ spacers of different lengths."
+ .
+ The reference to SMILE is made here especially because there is some
+ work done in the Debian Med SVN at
+ http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/?rev=0&sc=0
+ .
+ On the other hand the SMILE author told us in private mail that he
+ thinks that RISO is dead and SMILE continues to have some importance.
+
+Ignore: smile
+Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
+License: GPL
+WNPP: 221492
+Responsible: Steffen Moeller <moeller at debian.org>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/smile/trunk/
+Pkg-Description: Find statistically significant patterns in sequences
+ Smile determines sequence motifs on the basis of a set of DNA, RNA or
+ protein sequences. The work was originally described in the Journal of
+ Computational Biology (2000) 7:345-362 and has since been developed
+ further.
+ * No hard limit on the number of combinations of motifs to describe
+ subsets of sequences.
+ * The sequence alphabet may be specified.
+ * The use of wildcards is supported.
+ * Better determination of significance of motifs by simulation.
+ * Introduction of a set of sequences with negative controls
+ that should not match automatically determined motifs.
+ .
+ Note: We do not know anybody who actually uses SMILE and thus the
+ packaging effort is stalled. Feel free to tell us, if you are
+ interested in turning this into an official package.
+
+Depends: mummergpu
+Homepage: http://mummergpu.sourceforge.net/
+License: Artistic
+Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
+ The recent availability of new, less expensive high-throughput DNA
+ sequencing technologies has yielded a dramatic increase in the volume
+ of sequence data that must be analyzed. These data are being
+ generated for several purposes, including genotyping, genome
+ resequencing, metagenomics, and de novo genome assembly
+ projects. Sequence alignment programs such as MUMmer have proven
+ essential for analysis of these data, but researchers will need ever
+ faster, high-throughput alignment tools running on inexpensive
+ hardware to keep up with new sequence technologies.
+ .
+ MUMmerGPU is a low cost, ultra-fast sequence alignment program
+ designed to handle the increasing volume of data produced by new,
+ high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
+ replacement for MUMmer, using the GPUs in common workstations to
+ simultaneously align multiple query sequences against a single
+ reference sequence stored as a suffix tree. By processing the queries
+ in parallel on the highly parallel graphics card, MUMmerGPU achieves
+ more than a 10-fold speedup over a serial CPU version of the sequence
+ alignment kernel, and outperforms MUMmer on a high end CPU by
+ 3.5-fold in total application time when aligning reads from recent
+ sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
+ technologies.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: amos-assembler
+Homepage: http://amos.sourceforge.net/
+License: Artistic
+Pkg-Description: modular whole genome assembler
+ The AMOS consortium is committed to the development of open-source
+ whole genome assembly software. The project acronym (AMOS) represents
+ our primary goal -- to produce A Modular, Open-Source whole genome
+ assembler. Open-source so that everyone is welcome to contribute and
+ help build outstanding assembly tools, and modular in nature so that
+ new contributions can be easily inserted into an existing assembly
+ pipeline. This modular design will foster the development of new
+ assembly algorithms and allow the AMOS project to continually grow
+ and improve in hopes of eventually becoming a widely accepted and
+ deployed assembly infrastructure. In this sense, AMOS is both a
+ design philosophy and a software system.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: amoscmp
+Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
+License: Artistic
+Pkg-Description: comparative genome assembly package
+ A comparative assembler is a program that can assemble a set of
+ shotgun reads from an organism by mapping them to the finished
+ sequence of a related organism. Thus, a comparative assembler
+ transforms the traditional overlap-layout-consensus approach to
+ alignment-layout-consensus. The AMOScmp package uses the MUMmer
+ program to perform a mapping of the reads to the reference genome,
+ then processes the alignment results with a sophisticated layout
+ program designed to take into account polymorphisms between the two
+ genomes. For a detailed description of the algorithms involved please
+ refer to the paper listed in the References section.
+ .
+ AMOScmp uses as AMOS messages as both the inputs and the outputs (see
+ documentation). Two utilities are provided to process these files:
+ tarchive2amos - a versatile converter from trace archive .seq, .qual,
+ and .xml information into AMOS formatted data; amos2ace - a converter
+ from AMOS formatted data to the .ACE assembly format. In addition,
+ the AMOS::AmosLib Perl module is provided as a tool for users who
+ prefer to write their own conversion utilities. Please see the
+ documentation included with the distribution for more information.
+ .
+ AMOScmp is part of the AMOS package (see
+ http://amos.sourceforge.net/)- a collaborative effort to develop a
+ modular open-source framework for assembly development.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: minimus
+Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
+License: Artistic
+Pkg-Description: AMOS lightweight assembler
+ minimus is an assembly pipeline designed specifically for small
+ data-sets, such as the set of reads covering a specific gene. Note
+ that the code will work for larger assemblies (we have used it to
+ assemble bacterial genomes), however, due to its stringency, the
+ resulting assembly will be highly fragmented. For large and/or
+ complex assemblies the execution of Minimus should be followed by
+ additional processing steps, such as scaffolding.
+ .
+ minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
+ * overlapper - computes the overlaps between the reads using a
+ modified version of the Smith-Waterman local alignment algorithm
+ * tigger - uses the read overlaps to generate the layouts of reads
+ representing individual contigs
+ * make-consensus - refines the layouts produced by the tigger to
+ generate accurate multiple alignments within the reads
+ .
+ minimus uses as AMOS messages as both the inputs and the outputs (see
+ documentation). Two utilities are provided to process these files:
+ tarchive2amos - a versatile converter from trace archive .seq, .qual,
+ and .xml information into AMOS formatted data; amos2ace - a converter
+ from AMOS formatted data to the .ACE assembly format. In addition,
+ the AMOS::AmosLib Perl module is provided as a tool for users who
+ prefer to write their own conversion utilities. Please see the
+ documentation included with the distribution for more information.
+ .
+ minimus is part of the AMOS package - a collaborative effort to
+ develop a modular open-source framework for assembly development.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Ignore: catissuecore
+Homepage: https://cabig.nci.nih.gov/tools/catissuecore
+License: to be clarified, NCICB Open Source Project Site
+Pkg-Description: biospecimen inventory, tracking, and basic annotation
+ caTissue Core is caBIG's tissue bank repository tool for biospecimen
+ inventory, tracking, and basic annotation. Version 1.2.1 of caTissue
+ permits users to track the collection, storage, quality assurance,
+ and distribution of specimens as well as the derivation and
+ aliquotting of new specimens from an existing ones (e.g. for DNA
+ analysis). It also allows users to find and request specimens that
+ may then be used in molecular, correlative studies.
+ .
+ Intended Audiences: Translational Researchers, Pathologists, Biobank
+ Managers
+Note: A lot of stuff can be found at National Cancer Institute's
+ Center for Bioinformatics (NCICB) Open Source Project Site
+ http://gforge.nci.nih.gov/ which has to be evaluated and put into the
+ right category of our tasks files
+
+Ignore: trapss
+Homepage: https://putt.eng.uiowa.edu/
+License: Creative Commons for Science license
+Pkg-Description: Transcript Annotation Prioritization and Screening System
+ TrAPSS stands for Transcript Annotation Prioritization and Screening
+ System. It is a system comprised of several tools written by
+ researchers at the Coordinated Lab for Computational Genomics in the
+ University of Iowa. The system aims to aid scientists who are
+ searching for the genetic mutation or mutations that are linked to
+ expression of a disease phentotype. The system offers support for
+ almost all areas of a mutation discovery project from the creation
+ and prioritization of a large candidate gene list, to the selection,
+ ordering, and managing of primer pairs, and even support for SSCP
+ assay results. TrAPSS is a currently deployed and often used tool for
+ several laboratories here at the University of Iowa in the College of
+ Medicine. The system is composed of several Java applications, many
+ web-based PHP tools, and a local MySQL database. Even the Java
+ applications are available through a web browser due to Sun's Java
+ Web Start. Director of the CLCG, Professor Terry A. Braun, heads the
+ project along with Dr. Todd Scheetz and Prof. Thomas
+ L. Casavant. Eight developers create and maintain the software:
+ Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad;
+ along with three graduate students, Brian O'Leary, John Ritchison and
+ Michael Smith; and one undergraduate student, Matthew Kemp.
+ Importance of TrAPSS
+ .
+ The true importance of TrAPSS is that it is based upon a novel way to
+ examine a large candidate list of genes. Rather than sequentially
+ examining full genes, the scheme often followed in current target
+ identification projects, TrAPSS provides tools that offer the user
+ the opportunity to screen certain small parts of several genes from
+ the candidate list at once. This "parallel" screening idea was
+ envisioned by researchers here at the University of Iowa including
+ Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate
+ students Steven Davis and Brian O'Leary has demonstrated the
+ advantage of the parallel screening method over the sequential
+ sequencing of large candidate lists.
+Note: Found at
+ http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
+
+Depends: mage2tab
+Homepage: https://www.cbil.upenn.edu/magewiki/index.php/mage2tab
+License: CBIL Software and Data License (Apache-like)
+WNPP: 476209
+Responsible: Charles Plessy <plessy at debian.org>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mage2tab/trunk/
+Pkg-Description: MAGE-MLv1 converter and visualiser
+ This tool-kit is part of MR_T, a framework for import or export various of
+ MAGE (MicroArray Gene Expression) documents (MAGE-MLv1, MAGE-TAB, SOFT,
+ MINiML) from or into databases like GUS (the Genomics Unified Schema,
+ www.gusdb.org).
+
+Depends: bambus
+Homepage: http://amos.sourceforge.net/docs/bambus/
+License: Artistic
+Pkg-Description: hierarchical approach to building contig scaffolds
+ BAMBUS is the first publicly available scaffolding program. It orders
+ and orients contigs into scaffolds based on various types of linking
+ information. Additionally, BAMBUS allows the users to build scaffolds
+ in a hierarchical fashion by prioritizing the order in which links
+ are used. For more information please check out the online
+ documentation.
+ .
+ Note that currently Bambus is undergoing a transition in order to be
+ integrated with the AMOS package (see http://amos.sourceforge.net/)
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: hawkeye
+Homepage: http://amos.sourceforge.net/hawkeye/
+License: Artistic
+Pkg-Description: Interactive Visual Analytics Tool for Genome Assemblies
+ Genome assembly remains an inexact science. Even when accomplished
+ with the best software available, the assembly of a genome often
+ contains numerous errors, both small and large. Hawkeye is a visual
+ analytics tool for genome assembly analysis and validation, designed
+ to aid in identifying and correcting assembly errors. Hawkeye blends
+ the best practices from information and scientific visualization to
+ facilitate inspection of large-scale assembly data while minimizing
+ the time needed to detect mis-assemblies and make accurate judgments
+ of assembly quality.
+ .
+ All levels of the assembly data hierarchy are made accessible to
+ users, along with summary statistics and common assembly metrics. A
+ ranking component guides investigation towards likely mis-assemblies
+ or interesting features to support the task at hand. Wherever
+ possible, high-level overviews, dynamic filtering, and automated
+ clustering are leveraged to focus attention and highlight anomalies
+ in the data. Hawkeyes effectiveness has been proven on several genome
+ projects, where it has been used both to improve quality and to
+ validate the correctness of complex genomes.
+ .
+ Hawkeye is compatible with most widely used assemblers, including
+ Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
+ deposited in the NCBI Assembly Archive.
+ .
+ Publication: Schatz, M.C., Phillippy, A.M., Shneiderman, B.,
+ Salzberg, S.L. (2007) Hawkeye: a visual analytics tool for genome
+ assemblies. Genome Biology 8:R34.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: murasaki
+Homepage: http://murasaki.dna.bio.keio.ac.jp/
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/murasaki/trunk/
+Pkg-Description: homology detection tool across multiple large genomes
+ Murasaki is a scalable and fast, language theory-based homology
+ detection tool across multiple large genomes. It enable whole-genome
+ scale multiple genome global alignments. Supports unlimited length
+ gapped-seed patterns and unique TF-IDF based filtering.
+ .
+ Murasaki is an anchor alignment software, which is
+ * exteremely fast (17 CPU hours for whole Human x Mouse genome (with
+ 40 nodes: 52 wall minutes))
+ * scalable (Arbitrarily parallelizable across multiple nodes using MPI.
+ Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
+ * unlimited pattern length
+ * repeat tolerant
+ * intelligent noise reduction
+
+Depends: gmv
+Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
+License: GPL
+Pkg-Description: comparative genome browser for Murasaki
+ GMV is a comparative genome browser for Murasaki. GMV visualizes
+ anchors from Murasaki, annotation data from GenBank files, and
+ expression / prediction score from GFF files.
+
+Depends: pyrophosphate-tools
+Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
+License: not specified
+Pkg-Description: for assembling and searching pyrophosphate sequence data
+ Simple tools for assembling and searching high-density picolitre
+ pyrophosphate sequence data.
+
+Depends: figaro
+Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
+License: Artistic
+Pkg-Description: novel vector trimming software
+ Figaro is a software tool for identifying and removing the vector
+ from raw DNA sequence data without prior knowledge of the vector
+ sequence. By statistically modeling short oligonucleotide
+ frequencies within a set of reads, Figaro is able to determine which
+ DNA words are most likely associated with vector sequence. For a
+ description of Figaro's algorithms please see our paper. Figaro is
+ part of the AMOS suite.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+
+Depends: mirbase
+Homepage: http://microrna.sanger.ac.uk/
+License: Public Domain
+WNPP: 420938
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: The microRNA sequence database
+ The miRBase Sequence Database provides a searchable repository
+ for published microRNA sequences and associated annotation,
+ functionality previously provided by the microRNA Registry. miRBase
+ also contains predicted miRNA target genes in miRBase Targets, and
+ provides a gene naming and nomenclature function in the miRBase
+ Registry.
+ .
+ Release 9.1 of the database contains 4449 entries representing hairpin
+ precursor miRNAs, expressing 4274 mature miRNA products, in primates,
+ rodents, birds, fish, worms, flies, plants and viruses.
+ .
+ This package will install the miRBase database for mySQL, EMBOSS, and/or
+ ncbi-blast if you have the corresponding packages installed.
+ .
+ It is possible that mirbase will not be a package from the main archive, but
+ will be autogenerated as part of a larger data packaging effort.
+
+Depends: elph
+Homepage: http://www.cbcb.umd.edu/software/ELPH/
+License: Artistic
+Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
+ ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs
+ sampler for finding motifs in a set of DNA or protein sequences. The
+ program takes as input a set containing anywhere from a few dozen to
+ thousands of sequences, and searches through them for the most common
+ motif, assuming that each sequence contains one copy of the motif. We
+ have used ELPH to find patterns such as ribosome binding sites (RBSs)
+ and exon splicing enhancers (ESEs). See below for instructions on
+ downloading the complete system, including source code.
+ .
+ An online tool that uses ELPH output for identifying exon splicing
+ enhancers can be found at
+ http://www.cbcb.umd.edu/software/SeeEse/index.html .
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: repeatfinder
+Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
+License: Artistic
+Pkg-Description: finding repetitive sequences complete and draft genomes
+ Two programs for finding repeats in genomic DNA sequences. The first
+ program, described in the paper by Volfovsky et al. (2001) Genome
+ Biology is RepeatFinder. A second program, designed specifically to
+ find repeats likely to confuse a genome assembly, is called
+ ClosureRepeatFinder. The two programs are quite different and have
+ different purposes; RepeatFinder is intended to be the more
+ comprehensive approach. Note that RepeatFinder depends on Stefan
+ Kurtz's REPuter.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: reputer
+Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
+License: to be clarified
+Pkg-Description: fast computation of maximal repeats in complete genomes
+ A software tool was implemented that computes exact repeats and
+ palindromes in entire genomes very efficiently.
+Note: Download site (temporarily) not available - try to contact author
+
+Depends: transtermhp
+Homepage: http://transterm.cbcb.umd.edu/index.php
+License: Free
+Pkg-Description: finds rho-independent transcription terminators in bacterial genomes
+ finds rho-independent transcription terminators in bacterial
+ genomes. Each terminator found by the program is assigned a
+ confidence value that estimates its probability of being a true
+ terminator. TransTermHP is described in: C. Kingsford, K. Ayanbule
+ and S.L. Salzberg. Rapid, accurate, computational discovery of
+ Rho-independent transcription terminators illuminates their
+ relationship to DNA uptake. Genome Biology 8:R22 (2007).
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: patman
+Homepage: http://bioinf.eva.mpg.de/patman/
+License: GPL-2+
+WNPP: 482555
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: rapid alignment of short sequences to large databases
+ Patman searches for short patterns in large DNA databases, allowing
+ for approximate matches. It is optimized for searching for many small
+ pattern at the same time, for example microarray probes.
+
+Depends: uniprime
+Homepage: http://code.google.com/p/uniprime/
+License: GPL-3+
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: workflow-based platform for universal primer design
+ UniPrime automatically designs large sets of universal primers by simply
+ inputting a GeneID reference. It automatically retrieves and aligns
+ orthologous sequences from GenBank, identifies regions of conservation within
+ the alignment and generates suitable primers that can amplify variable genomic
+ regions. UniPrime differs from previous automatic primer design programs in
+ that all steps of primer design are automated, saved and are phylogenetically
+ limited. We have experimentally verified the efficiency and success of this
+ program. UniPrime is an experimentally validated, fully automated program that
+ generates successful cross-species primers that take into account the
+ biological aspects of the PCR.
+
+Depends: genetrack
+Homepage: http://sysbio.bx.psu.edu/genetrack.html
+License: MIT
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: genomic data storage and visualization framework
+ GeneTrack is a high performance bioinformatics data storage and analysis
+ system designed to store genome wide information. It is currently used to
+ analyze data obtained via high-throughput rapid sequencing platforms such as
+ the 454 and Solexa as well as tiling array data based on various platforms.
+
+Depends: operondb
+Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
+License: to be clarified
+Pkg-Description: detect and analyze conserved gene pairs
+ Comparison of complete microbial genomes reveals a large number of
+ conserved gene clusters - sets of genes that have the same order in
+ two or more different genomes. Such gene clusters often, but not
+ always represent a co-transcribed unit, or operon. A method was
+ developed to detect and analyze conserved gene pairs - pairs of genes
+ that are located close on the same DNA strand in two or more
+ bacterial genomes. For each conserved gene pair, an estimate of
+ probability is calculated that the genes belong to the same
+ operon. The algorithm takes into account several alternative
+ possibilities. One is that functionally unrelated genes may have the
+ same order due simply because they were adjacent in a common
+ ancestor. Other possibilities are that genes may be adjacent in two
+ genomes by chance alone, or due to horizontal transfer of the gene
+ pair.
+ .
+ The method is modified from the one described in: Maria D. Ermolaeva,
+ Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
+ Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
+ .
+ OperonDB was supported by the NIH under grant R01-LM007938 and by the
+ NSF under grant DBI-0234704.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
+ no info about license or downloadable code found, but tried to
+ contact authors.
+
+Depends: trnascan-se
+Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/
+License: GPL
+Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence
+ tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence
+ while giving less than one false positive per 15 gigabases. Two
+ previously described tRNA detection programs are used as fast,
+ first-pass prefilters to identify candidate tRNAs, which are then
+ analyzed by a highly selective tRNA covariance model. This work
+ represents a practical application of RNA covariance models, which
+ are general, probabilistic secondary structure profiles based on
+ stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000
+ bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA
+ homologues such as selenocysteine tRNAs, tRNA-derived repetitive
+ elements and tRNA pseudogenes.
+
+Depends: beast-mcmc
+Homepage: http://beast.bio.ed.ac.uk/
+License: LGPL
+Pkg-Description: Bayesian MCMC analysis of molecular sequences
+ BEAST is a cross-platform program for Bayesian MCMC analysis of
+ molecular sequences. It is entirely orientated towards rooted,
+ time-measured phylogenies inferred using strict or relaxed molecular
+ clock models. It can be used as a method of reconstructing
+ phylogenies but is also a framework for testing evolutionary
+ hypotheses without conditioning on a single tree topology. BEAST uses
+ MCMC to average over tree space, so that each tree is weighted
+ proportional to its posterior probability. We include a simple to use
+ user-interface program for setting up standard analyses and a suit of
+ programs for analysing the results.
+ .
+ The source is avialable at http://code.google.com/p/beast-mcmc/ .
+Remark: Name space pollution
+ There is a Debian package beast which is completely unrelated
+ to this project.
+
+Depends: artemis
+Homepage: http://www.sanger.ac.uk/Software/Artemis/
+License: GPL 2+
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: genome viewer and annotation tool
+ Artemis is a free genome viewer and annotation tool that allows visualization
+ of sequence features and the results of analyses within the context of the
+ sequence, and its six-frame translation. Artemis is written in Java, and is
+ available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK
+ database entries or sequence in FASTA or raw format. Extra sequence features
+ can be in EMBL, GENBANK or GFF format.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: srf
+Homepage: http://srf.sourceforge.net/
+License: Apache License V2.0
+WNPP: 489983
+Responsible: Charles Plessy <plessy at debian.org>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/srf/trunk/
+Pkg-Description: C++ implementation of the SRF format for DNA sequence data
+ SRF (sort for Sequence Read Format) is a generic format capable of storing
+ data generated by any DNA sequencing technology. Hence it has sufficient
+ flexibility to store data from current and future DNA sequencing technologies
+ at minimal cost of implementation. Benefits include a single input file format
+ for all downstream applications and a read lookup index enabling downstream
+ formats to reference reads without duplication of all of the read specific
+ information.
+ .
+ This package contains the version 1.3 and the draft of the version
+ 1.3.1 of the SRF specification.
+ .
+ This splits up into a library package which reads the format and a
+ doc package which documents to format.
+
+Depends: alien-hunter
+Homepage: http://www.sanger.ac.uk/Software/analysis/alien_hunter/
+License: GPL
+Pkg-Description: Interpolated Variable Order Motifs for identification of horizontally acquired DNA
+ alien_hunter is an application for the prediction of putative
+ Horizontal Gene Transfer (HGT) events with the implementation of
+ Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits
+ compositional biases using variable order motif distributions and
+ captures more reliably the local composition of a sequence compared
+ to fixed-order methods. Optionally the predictions can be parsed into
+ a 2-state 2nd order Hidden Markov Model (HMM), in a change-point
+ detection framework, to optimize the localization of the boundaries
+ of the predicted regions. The predictions (embl format) can be
+ automatically loaded into Artemis genome viewer freely available at:
+ http://www.sanger.ac.uk/Software/Artemis/.
+ .
+ The manuscript describing the alien_hunter algorithm is available
+ from Bioinformatics: Interpolated variable order motifs for
+ identification of horizontally acquired DNA: revisiting the
+ Salmonella pathogenicity islands. Vernikos GS, Parkhill J
+ Bioinformatics. 2006;. PMID: 16837528
+Remark: Archive contains outdated copy of BioJava
+ The archive contains biojava 1.4 - but we it was working
+ successfully with the Debian packaged version of BioJava.
+ So stripping the copy of BioJava from the source package
+ seem to be a good idea.
+
+Depends: act
+Homepage: http://www.sanger.ac.uk/Software/ACT/
+License: GPL
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-Description: DNA Sequence Comparison Viewer
+ ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer
+ based on Artemis. In common with Artemis, ACT is written in Java and
+ runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can
+ read complete EMBL and GENBANK entries or sequence in FASTA or raw
+ format. Extra sequence features can be in EMBL, GENBANK or GFF
+ format.
+ .
+ The sequence comparison displayed by ACT is usually the result of
+ running a blastn or tblastx search. See the user manual for more
+ information.
+ .
+ To see ACT in action go to the examples page
+ http://www.sanger.ac.uk/Software/ACT/Examples/
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: samtools
+Homepage: http://samtools.sourceforge.net
+License: MIT
+WNPP: 540453
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/samtools/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/samtools/trunk/
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: Processing sequence alignments in SAM format.
+ Samtools is a set of utilities that manipulate alignments in the BAM format.
+ It imports from and exports to the SAM (Sequence Alignment/Map) format, does
+ sorting, merging and indexing, and allows to retrieve reads in any regions
+ swiftly.
+
+Depends: acedb-other-dotter, acedb-other-belvu
+
+Depends: acedb-other
+Homepage: http://www.acedb.org/
+License: GPL / LGPL
+Language: C, C++
+WNPP: 542068
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/acedb/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/acedb/trunk/
+Responsible: Steffen Moeller <moeller at debian.org>
+Pkg-Description: tools designed to manipulate genomic data
+ AceDB is a genome database system developed since 1989 primarily by
+ Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger
+ Institute). It provides a custom database kernel, with a non-standard
+ data model designed specifically for handling scientific data
+ flexibly, and a graphical user interface with many specific displays
+ and tools for genomic data. AceDB is used both for managing data
+ within genome projects, and for making genomic data available to the
+ wider scientific community.
+ .
+ AceDB was originally developed for the C.elegans genome project ,
+ from which its name was derived (A C. elegans DataBase). However, the
+ tools in it have been generalized to be much more flexible and the
+ same software is now used for many different genomic databases from
+ bacteria to fungi to plants to man. It is also increasingly used for
+ databases with non-biological content.
+
+Comment: If you stumble upon alfresco at
+ http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
+ tarball vanished from the downlowad page. So this is not for us even
+ if it is linked from Sanger Institute web site.
+
+Comment: If you stumble upon angler at
+ http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because
+ it is not updated since 1997. I found no license statement and so
+ this is probably also not for us except somebody has real interest
+ and volunteers to clarify the license.
+
+Depends: cdna-db
+Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
+License: Artistic
+Pkg-Description: quality-control checking of finished cDNA clone sequences
+ cdna_db is a software system designed for quality-control checking of
+ finished cDNA clone sequences, and their computational analysis. The
+ combination of a relational db (MySQL) schema, and an
+ object-orientated perl API make it easy to implement high-level
+ analyses of these transcript sequences.
+ .
+ The cdna_db can store cDNA clone sequences, and ESTs and
+ consensus/contig sequences also derived from these clones. These are
+ then used by the system to check cDNA clone sequence identity etc
+ (see deneral_doc.txt). For each clone multiple DNA sequence versions
+ can be stored, if for instance, the finished DNA sequence is revised
+ as part of the sequencing process.
+ .
+ A blast pipeline is implemented together with a job control system
+ (with LSF underlying) so that multiple CPUs can be used in parallel
+ to carry out the blasts of large datasets. The searches can be made
+ incremental, so as more cDNA sequences are added to the databank,
+ just the new clones are blasted.
+ .
+ Utility scripts are provided to delete previous search results, and
+ dump cDNA clones sequences (such as those that passed the QC
+ checking) from the cdna_db.
+
+Depends: das-proserver
+Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
+License: Same as Perl
+Pkg-Description: lightweight Distributed Annotation System (DAS) server
+ The Distributed Annotation System (DAS) is a data exchange protocol
+ for open sharing of biological information.
+ .
+ ProServer is a very lightweight DAS server written in Perl. It is
+ simple to install and configure and has existing adaptors for a wide
+ variety of data sources. It is also easily extensible allowing
+ adaptors to be written for other data sources. More information about
+ the DAS protocol and what it is useful for is available over at
+ http://biodas.org.
+ .
+ New large scale techniques in biology are producing a rapidly growing
+ amount of public available data. Centralized database resources are
+ confronted with the task how to scale their storage facilities, how
+ to manage frequent updates and how to exchange the data with the
+ community.
+ .
+ The Distributed Annotation System (DAS) addresses these issues. It is
+ frequently being used to openly exchange biological annotations
+ between distributed sites. Data distribution, performed by DAS
+ servers, is separated from visualization, which is done by DAS
+ clients.
+ .
+ DAS is a client-server system in which a client like Ensembl
+ integrates information from multiple servers. It allows a single
+ machine to gather up genome annotation information from multiple
+ distant web sites, collate the information, and display it to the
+ user in a single view. Little coordination is needed among the
+ various information providers.
+ .
+ DAS is heavily used in the genome bioinformatics community. Over the
+ last years we have also seen growing acceptance in the protein
+ sequence and structure communities.
+
+Depends: spice
+Homepage: http://www.efamily.org.uk/software/dasclients/spice/
+License: GPL
+Pkg-Description: Distributed Annotation System (DAS) client
+ The Distributed Annotation System (DAS) is a data exchange protocol
+ for open sharing of biological information.
+ .
+ SPICE is a browser for protein sequences, structures and their
+ annotations. It can display annotations for PDB, UniProt and Ensembl
+ Peptides. All data is retrieved from different sites on the Internet,
+ that make their annotations available using the DAS protocol. It is
+ possible to add new annotations to SPICE, and to compare them with
+ the already available information.
+
+Depends: decipher
+Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
+License: To be clarified
+Pkg-Description: tracks duplications and deletions of DNA in patients
+ DECIPHER tracks submicroscopic duplications and deletions of DNA in
+ patients together with phenotypes exhibited by those
+ patients. DECIPHER tallies these genetic abnormalities with genes and
+ other features of interest in the affected areas. The aim of DECIPHER
+ is to provide a research tool to aid clinical diagnosis and treatment
+ of these conditions. DECIPHER makes use of DAS technology to
+ integrate with Ensembl, the world's leading genome browser.
+
+Depends: est-db
+Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
+License: Artistic
+Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
+ The est_db package is a software suite and database system designed
+ to support expressed sequence tag (EST) sequencing projects, and to
+ provide comprehensive bioinformatic analysis of sequenced EST
+ libraries, for gene discovery and other purposes. The database can
+ hold and efficiently process hundreds of thousands of EST sequences,
+ track the cDNA libraries and clones to which they belong, and store
+ the results of their analysis. Should they be available, large
+ compute farms can be used for the analysis.
+ .
+ Extensive bioinformatic analysis can be carried out on the sequenced
+ EST libraries, including similarity (BLAST) searches, protein
+ sequence prediction, and the import of EST clustering and assembly
+ data from external sources. Results are searchable via a web page,
+ with graphic output of the various analyses, enabling one to retrieve
+ information pertaining to a particular cDNA clone, or EST read, as
+ well as view EST clustering results, or graphical representations of
+ BLAST results on the searched EST sequences.
+ .
+ The est_db package is likely to appeal not only to sequencing groups
+ directly employed in EST sequencing, but also to groups interested in
+ performing bespoke analysis of ESTs that may already be publically
+ available, in order to support their ongoing research aims. The
+ package is easily-extensible, via an API designed specifically to
+ handle ESTs and their analysis. It is open source and is made
+ available free of charge, and, where possible, similarly
+ open-licensed components have been used in its development.
+
+Depends: finex
+Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
+License: To be clarified
+Pkg-Description: sequence homology searching
+ The FINEX program allows sequence homology searching techniques to be
+ applied, where the sequence data is replaced with a fingerprint
+ abstracted from the intron/exon boundary phase and the exon length.
+ .
+ Please note FINEX is no longer supported but is available for
+ download.
+
+Depends: hexamer
+Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
+License: GPL
+Pkg-Description: scan DNA sequences to look for likely coding regions
+ Hexamer is a program to scan DNA sequences to look for likely coding
+ regions. The principle is to use 6mers, but to avoid deriving any
+ information from base composition. Therefore, the frequencies of each
+ 6mer are normalized by dividing by the total frequency of all 6mers
+ with the same base composition.
+ .
+ There are two programs involved in this process:
+ * hextable
+ hextable makes files of statistics that hexamer uses to scan for
+ likely coding regions.
+ The input of hextable is a fasta file of coding sequences in
+ frame. The -o file output is an ascii list of 4096 floating point
+ numbers giving log likelihood ratio scores in bits. The output on
+ stdout is a summary of the information content of the table,
+ indicating how disriminative it is likely to be.
+ * hexamer
+ Uses the .hex file from hextable to scan a DNA sequence for likely
+ coding regions.
+ The input is a fasta DNA file (n.b. that these programs assume all
+ 'a','c','g','t'. 'n's found in the sequence files will be
+ converted to 'c'.
+ The output of hexamer is in General Feature Format (GFF) format.
+
+Depends: logomat-m
+Homepage: http://www.sanger.ac.uk/Software/analysis/logomat-m/
+License: As Perl itself
+Pkg-Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).
+ .
+ If you use HMM-Logos in your publication, please cite HMM Logos for
+ visualization of protein families. Schuster-B"ockler B, Schultz J,
+ Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
+ 10.1186/1471-2105-5-7
+
+Depends: coot
+Homepage: http://www.ysbl.york.ac.uk/~emsley/coot/
+License: GPL
+Pkg-Description: protein structure model-building, -completion, -validation
+ The Crystallographic Object-Oriented Toolkit (Coot) displays maps and
+ models and allows model manipulations such as idealization, real space
+ refinement, manual rotation/translation, rigid-body fitting, ligand
+ search, solvation, mutations, rotamers, Ramachandran plots...
+
+Depends: r-ape
+Homepage: http://ape.mpl.ird.fr/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Analyses of Phylogenetics and Evolution
+ APE (Analyses of Phylogenetics and Evolution) is a package written in R.
+ APE aims to be both a computing tool to analyse phylogenetic and
+ evolutionary data, and an environment to develop and implement new
+ analytical methods.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: caftools
+Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
+License: Free for non-commercial purposes
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Tools to maintain DNA sequence assemblies
+ This is V2 of the CAF (Common Assembly Format) C-tools. It comprises
+ a set of libraries and programs for manipulating DNA sequence
+ assemblies using CAF files.
+ .
+ The CAF specification can be found at:
+ http://www.sanger.ac.uk/Software/formats/CAF/
+Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.
+
+Depends: roche454ace2caf
+Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
+License: not specified
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: convert GS20 or FLX assemblies into CAF format
+ Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
+ CAF format so that these are correct viewable/editable/... whithin
+ the staden package (gap4). You have then access to "hidden data",
+ exact aligned trace and there positions, base values etc and whith
+ staden-1-7-0 you have graphical access to the associated flowgramm
+ traces (SFF format).
+ .
+ Description, Goals - please take a look at
+ http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
+Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.
+
+Depends: big-blast
+Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Helper tool to run blast on large sequences
+ This script will chop up a large sequence, run blast on each bit and
+ then write out an EMBL feature table and a MSPcrunch -d file
+ containing the hits.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: blixem
+Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
+License: not specified
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: interactive browser of pairwise Blast matches
+ Blixem (BLast matches In an X-windows Embedded Multiple alignment),
+ is an interactive browser of pairwise Blast matches that have been
+ stacked up in a ma ster-slave multiple alignment
+Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source.
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: cap3
+Homepage: http://genome.cs.mtu.edu/cap/cap3.html
+License: free for governmental agency or a non-profit educational institution
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: DNA Sequence Assembly Program
+ CAP3 contains the following improvements to the CAP sequence assembly
+ program.
+ 1. Use of forward-reverse constraints to correct assembly errors and
+ link contigs.
+ 2. Use of base quality values in alignment of sequence reads.
+ 3. Automatic clipping of 5' and 3' poor regions of reads.
+ 4. Generation of assembly results in ace file format for Consed.
+ 5. CAP3 can be used in GAP4 of the Staden package.
+ These improvements allow CAP3 to take longer sequences of higher
+ errors and produce more accurate consensus sequences.
+Remark: Obtaining the source requires to fill in a registration form
+ Official distribution in Debian is probably impossible. The
+ package included in the BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html containins only the binaries
+ cap3 and formcon, dated Aug 29, 2002. This package exists purely for
+ convenience to Bio-Linux users so that the files are placed in
+ locations consistent with the Bio-Linux setup.
+
+Depends: cd-hit
+Homepage: http://www.bioinformatics.org/cd-hit/
+License: to be clarified
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: suite of programs designed to quickly group sequences.
+ CD-HIT stands for Cluster Database at High Identity with
+ Tolerance. The program (cd-hit) takes a fasta format sequence
+ database as input and produces a set of 'non-redundant' (nr)
+ representative sequences as output. In addition cd-hit outputs a
+ cluster file, documenting the sequence 'groupies' for each nr
+ sequence representative. The idea is to reduce the overall size of
+ the database without removing any sequence information by only
+ removing 'redundant' (or highly similar) sequences. This is why the
+ resulting database is called non-redundant (nr). Essentially, cd-hit
+ produces a set of closely related protein families from a given fasta
+ sequence database.
+ .
+ CD-HIT uses a 'longest sequence first' list removal algorithm to
+ remove sequences above a certain identity threshold. Additionally the
+ algorithm implements a very fast heuristic to find high identity
+ segments between sequences, and so can avoid many costly full
+ alignments.
+ .
+ With recent developments, cd-hit package offers new programs for DNA
+ sequence clustering and comparing two databases. It also has lots of
+ new options for clustering control.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Comment: BioLinux contains a clcworkbench package which is available
+ at http://www.clcbio.com/index.php?id=28 but this seems to be only
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: coalesce
+Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: outdated program to estimate population-genetic parameters
+ COALESCE fits the model which has a single population of constant
+ size, and estimates 4Nu, where N is the effective population size and
+ u is the neutral mutation rate per site. You may also want the
+ Postscript or the TeX file of the preprint version of the Kuhner,
+ Yamato, and Felsenstein 1995 paper.
+Remark: This software is probably outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting COALESCE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however." So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Comment: BioLinux contains a dendroscope package which is available
+ at http://www.dendroscope.org but this project has only a
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: dotter
+Homepage: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detailed comparison of two sequences
+ Dotter is a graphical dotplot program for detailed comparison of two
+ sequences. Here, every residue in one sequence is compared to every
+ residue in the other sequence. The first sequence runs along the
+ x-axis and the second sequence along the y-axis. In regions where the
+ two sequences are similar to each other, a row of high scores will
+ run diagonally across the dot matrix. If you're comparing a sequence
+ against itself to find internal repeats, you'll notice that the main
+ diagonal scores maximally, since it's the 100% perfect self-match.
+ .
+ To make the score matrix more intelligible, the pairwise scores are
+ averaged over a sliding window which runs diagonally. The averaged
+ score matrix forms a three-dimensional landscape, with the two
+ sequences in two dimensions and the height of the peaks in the
+ third. This landscape is projected onto two dimensions by aid of
+ greyscales - the darker grey of a peak, the higher it is.
+ .
+ Dotter provides a tool to explore the visual appearance of this
+ landscape, as well as a tool to examine the sequence alignment it
+ represents.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+ .
+ Homepage is currently unavailable but the source might be
+ obtainable from freebsd.org.
+
+Depends: dotur
+Homepage: http://schloss.micro.umass.edu/software/dotur.html
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Defining Operational Taxonomic Units and estimating species Richness
+ Dotur (Distance Based OTU and Richness determination) is a computer
+ program that takes a distance matrix describing the genetic distance
+ between DNA sequence data and assigns sequences to operational
+ taxonomic units (OTUs) using either the furthest, average, or nearest
+ neighbor algorithms for all possible distances that can be described
+ using the distance matrix. Using the OTU composition data, dotur
+ constructs collector's and rarefaction curves for sampling intensity,
+ richness estimators, and diversity indices.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: estferret
+Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
+License: to be clarified
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: processes, clusters and annotates EST data
+ ESTFerret processes, clusters and annotates EST data. It is
+ user-configurable. Results are currently stored in a series of text
+ tables. Annotation consists of searches against use r-defined blast
+ databases, prosite, GO and allocation of EC numbers where possible.
+ .
+ EST-ferret is a user-configurable, automated pipeline for the
+ convenient analysis of EST sequence data that includes all of the
+ necessary steps for cleanup and trimming, submission to external
+ sequence repositories, clustering, identification by BLAST homology
+ searches and by searches of protein domain databases, annotation with
+ computer-addressable terms and production of outputs for direct entry
+ into microarray analysis packages. It is composed of several widely
+ used, open-source algorithms, including PHRED, CAP3, BLAST, and a
+ range of sequence and annotation databases, including Gene Ontology
+ and Conserved Domain Database to deliver a putative identity and a
+ detailed annotation of each clone. It can be run either step-by-step
+ to track the outputs, or as a single batch process. Users can easily
+ edit the configuration file to define parameter settings.
+ .
+ This package has five major components: (1) ESTs coding system; (2)
+ sequence processing; (3) sequence clustering; (4) sequence annotating
+ and (5) storage and reporting of results. DNA trace files are renamed
+ and converted into FASTA format, cleaned and submitted to
+ dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
+ CAP3 to assemble the ESTs into groups corresponding to separate gene
+ families and unique genes. Sequence identification and annotation is
+ provided by a series of BLAST homology searches (Parallel_BLAST and
+ Priority_BLAST) against user-defined sequence databases implemented
+ with the NCBI BLASTALL algorithm. The BLAST results are parsed and
+ annotation terms that reflect functional attributes are captured from
+ Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
+ Commission (EC) databases and applied to each of the clones. CDD (and
+ InterPro) searches are performed for seeking protein domains in the
+ sequences. Other options are provided to run PatSearch, RepeatMasker
+ and BLAT to find UTRs, repeats and EST candidates in
+ genomes. Finally, the package generates analysis reports in a variety
+ of flat file formats, sources of which can be serve as inputs for
+ some gene annotation and gene expression profiling tools, and also as
+ a MySQL database or web-browsable search tool.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: estscan
+Homepage: http://estscan.sourceforge.net/
+License: free
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detect coding regions in DNA sequences, even if of low quality
+ ESTScan is a program that can detect coding regions in DNA sequences,
+ even if they are of low quality. It will also detect and correct
+ sequencing errors that lead to fr ameshifts.
+ .
+ ESTScan is not a gene prediction program, nor is it an open reading
+ frame detector. In fact, its strength lies in the fact that it does
+ not require an open reading frame to detect a coding region. As a
+ result, the program may miss a few translated amino acids at either
+ the N or the C terminus, but will detect coding regions with high
+ selectivity and sensitivity.
+ .
+ Similarly to GENSCAN, ESTScan uses a Markov model to represent the
+ bias in hexanucleotide usage found in coding regions relative to
+ non-coding regions. Additionally, ESTScan allows insertions and
+ deletions when these improve the coding region statistics. Further
+ details can be found at:
+ http://www.ch.embnet.org/software/ESTScan2_help.html
+ .
+ References:
+ * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing
+ errors by combining Hidden Markov models Bioinformatics 19,
+ ii103-ii112.
+ * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
+ detecting, evaluating, and reconstructing potential coding regions in
+ EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: fasta
+Homepage: http://www.ebi.ac.uk/Tools/fasta/
+License: no inclusion into commercial product
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: searching DNA and protein databases
+ FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact
+ that it can be used for a fast protein comparison or a fast
+ nucleotide comparison. This program achieves a high level of
+ sensitivity for similarity searching at high speed. This is achieved
+ by performing optimised searches for local alignments using a
+ substitution matrix. The high speed of this program is achieved by
+ using the observed pattern of word hits to identify potential matches
+ before attempting the more time consuming optimised search. The
+ trade-off between speed and sensitivity is controlled by the ktup
+ parameter, which specifies the size of the word. Increasing the ktup
+ decreases the number of background hits. Not every word hit is
+ investigated but instead initially looks for segment's containing
+ several nearby hits.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: fluctuate
+Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: outdated program to model a single population
+ FLUCTUATE fits the model which has a single population which has been
+ growing (or shrinking) according to an exponential growth law. It
+ estimates 4Nu and g, where N is the effective population size, u is
+ the neutral mutation rate per site, and g is the growth rate of the
+ population.
+Remark: This software is probably outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting FLUCTUATE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however." So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Depends: forester
+Homepage: http://sourceforge.net/projects/forester-atv/
+License: LGPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: visualization of annotated phylogenetic trees
+ FORESTER is a Java/Perl based software package for phylogenomic
+ analyses. Currently, it includes the phylogenetic tree visualization
+ and manipulation tool ATV and implementations of the SDI algorithm
+ and the RIO method (http://www.phylosoft.org/).
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: r-other-mott-happy
+Homepage: http://www.well.ox.ac.uk/happy/happyR.shtml
+License: GPL
+WNPP: 530007
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/
+Responsible: Steffen Moeller <moeller at debian.org>
+Pkg-Description: GNU R package for fine-mapping complex diseases
+ The idea behind this package is that when multiple strains of
+ animals that differ in their susceptibility to multiple diseases
+ are bread over multiple generations, then one can analyse the
+ contribution that a particular genetic locus has to each of those
+ diseases. While in the past this approach has been performed
+ for one disease at a time, this tool extends the statistics
+ for allowing multiple crosses and thus save animal lifes. A larger
+ stock of animals with more generations to keep them will further
+ help producing larger numbers of observable cross-over events
+ and thus help increasing the resolution of the mapping.
+ .
+ happy is an R interface into the HAPPY C package for fine-mapping
+ Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is
+ an advanced intercross between (usually eight) founder inbred strains
+ of mice. HS are suitable for fine-mapping QTL. The happy package is
+ an extension of the original C program happy; it uses the C code to
+ compute the probability of descent from each of the founders, at each
+ locus position, but the happy packager allows a much richer range of
+ models to be fit to the data.
+
+Depends: jalview
+Homepage: http://www.jalview.org/
+License: GPL
+WNPP: 507436
+Responsible: Vincent Fourmond <fourmond at debian.org>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: multiple alignment editor
+ Jalview is a multiple alignment editor written in Java. It is used
+ widely in a variety of web pages (e.g. the EBI Clustalw server and
+ the Pfam protein domain database) but is available as a general
+ purpose alignment editor.
+
+Depends: lamarc
+Homepage: http://evolution.gs.washington.edu/lamarc/
+License: Apache V2.0
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimate population-genetic parameters
+ LAMARC is a program which estimates population-genetic parameters
+ such as population size, population growth rate, recombination rate,
+ and migration rates. It approximates a summation over all possible
+ genealogies that could explain the observed sample, which may be
+ sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
+ its sister program Migrate are successor programs to the older
+ programs Coalesce, Fluctuate, and Recombine, which are no longer
+ being supported. The programs are memory-intensive but can run
+ effectively on workstations.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: lucy
+Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: DNA sequence quality and vector trimming tool
+ Lucy is a utility that prepares raw DNA sequence fragments for
+ sequence assembly, possibly using the TIGR Assembler. The cleanup
+ process includes quality assessment, confidence reassurance, vector
+ trimming and vector removal. The primary advantage of Lucy over other
+ similar utilities is that it is a fully integrated, stand alone
+ program.
+ .
+ Lucy was designed and written at The Institute for Genomic Research
+ (TIGR, now the J. Craig Venter Institute), and it has been used here
+ for several years to clean sequence data from automated DNA
+ sequencers prior to sequence assembly and other downstream uses. The
+ quality trimming portion of lucy makes use of phred quality scores,
+ such as those produced by many automated sequencers based on the
+ Sanger sequencing method. As such, lucy’s quality trimming may not
+ be appropriate for sequence data produced by some of the new
+ “next-generation†sequencers.
+ .
+ See also the SourceForge page at http://lucy.sourceforge.net/.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: maxd
+Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
+License: Artistic
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: data warehouse and visualisation environment for genomic expression data
+ Maxd is a data warehouse and visualisation environment for genomic
+ expression data. It is being developed in the University of
+ Manchester by the Microarray Bioinformatics Group.
+ .
+ Software components:
+ maxdLoad2 - standards-compliant, highly customisable transcriptomics
+ database
+ maxdView - modular and easily extensible data visualisation and
+ analysis environment
+ maxdSetup - installation management utility
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: mesquite
+Homepage: http://mesquiteproject.org/mesquite/mesquite.html
+License: LGPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: help biologists analyze comparative data about organisms
+ Mesquite is software for evolutionary biology, designed to help
+ biologists analyze comparative data about organisms. Its emphasis is
+ on phylogenetic analysis, but some of its modules concern population
+ genetics, while others do non-phylogenetic multivariate
+ analysis. Because it is modular, the analyses available depend on the
+ modules installed. Analyses include:
+ * Reconstruction of ancestral states (parsimony, likelihood)
+ * Tests of process of character evolution, including correlation
+ * Analysis of speciation and extinction rates
+ * Simulation of character evolution (categorical, DNA, continuous)
+ * Parametric bootstrapping (integration with programs such as PAUP*
+ and NONA)
+ * Morphometrics (PCA, CVA, geometric morphometrics)
+ * Coalescence (simulations, other calculations)
+ * Tree comparisons and simulations (tree similarity, Markov
+ speciation models)
+ There is a brief outline of features, which includes
+ screenshots. Mesquite is not primarily designed to infer phylogenetic
+ trees, but rather for diverse analyses using already inferred trees.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: migrate
+Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
+License: to be clarified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimation of population sizes and gene flow using the coalescent
+ Migrate estimates effective population sizes and past migration rates
+ between n population assuming a migration matrix model with
+ asymmetric migration rates and different subpopulation sizes. Migrate
+ uses maximum likelihood or Bayesian inference to jointly estimate all
+ parameters. It can use the followind data types: sequence data using
+ Felsenstein's 84 model with or without site rate variation, single
+ nucleotide polymorphism data, microsatellite data using a stepwise
+ mutation model or a brownian motion mutation model, and
+ electrophoretic data using an 'infinite' allele model. The output can
+ contain: Estimates of all migration rates and all population sizes,
+ assuming constant mutation rates among loci or a gamma distributed
+ mutation rate among loci. Profile likelihood tables, Percentiles,
+ Likelihood-ratio tests, and simple plots of the log-likelihood
+ surfaces for all populations and all loci.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: mrbayes
+Homepage: http://mrbayes.csit.fsu.edu/
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Bayesian estimation of phylogeny
+ MrBayes is a program for the Bayesian estimation of
+ phylogeny. Bayesian inference of phylogeny is based upon a quantity
+ called the posterior probability distribution of trees, which is the
+ probability of a tree conditioned on the observations. The
+ conditioning is accomplished using Bayes's theorem. The posterior
+ probability distribution of trees is impossible to calculate
+ analytically; instead, MrBayes uses a simulation technique called
+ Markov chain Monte Carlo (or MCMC) to approximate the posterior
+ probabilities of trees.
+ .
+ The program takes as input a character matrix in a NEXUS file
+ format. The output is several files with the parameters that were
+ sampled by the MCMC algorithm. MrBayes can summarize the information
+ in these files for the user. The program features include:
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: msatfinder
+Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: identification and characterization of microsatellites in a comparative genomic context
+ Msatfinder is a Perl script designed to allow the identification and
+ characterization of microsatellites in a comparative genomic
+ context. There is also an online manual, a discussion forum and an
+ online interface where users can do searches in any number of DNA or
+ protein sequences (as long as the maximum size of all sequences does
+ not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
+ FASTA, EMBL and Swissprot formats are supported.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: mview
+Homepage: http://bio-mview.sourceforge.net/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: reformat results of a sequence database search or a multiple alignment
+ MView is a tool for converting the results of a sequence database
+ search (BLAST, FASTA, etc.) into the form of a coloured multiple
+ alignment of hits stacked against the query. Alternatively, an
+ existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be pr
+ ocessed. It reformats the results of a sequence database search or a
+ multiple alignment adding optional HTML markup to control colouring
+ and web page layout. MView is not a multiple alignment program, nor
+ is it a general purpose alignment editor.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: oligoarrayaux
+Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
+License: non-free (fre academical use)
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Prediction of Melting Profiles for Nucleic Acids
+ OligoArrayAux is a subset of the UNAFold package for use with
+ OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray
+ is a free software that computes gene specific oligonucleotides for
+ genome-scale oligonucleotide microarray construction. (It is not
+ really specified what they mean with "free software". You can
+ download the source code after registration: "registration is the
+ only way for me to keep trace of OligoArray users and be able to send
+ you a bug fix or a new release".)
+ .
+ The original UNAFold server is available at
+ http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
+ read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
+ "Prediction of Melting Profiles for Nucleic Acids".
+Remark: This package is included into BioLinux distribution
+ Finally it is hard to find some documentation what OligoArrayAux is
+ really doing because it is only specified into relation to OligoArray
+ (as precondition) and UNAFold (as subset of this) but BioLinux
+ distribution http://envgen.nox.ac.uk/biolinux.html decided to package
+ this and so it might make soem sense to list it here - further
+ investigation is needed.
+
+Depends: omegamap
+Homepage: http://www.danielwilson.me.uk/software.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detecting natural selection and recombination in DNA or RNA sequences
+ OmegaMap is a program for detecting natural selection and
+ recombination in DNA or RNA sequences. It is based on a model of
+ population genetics and molecular evolution. The signature of natural
+ selection is detected using the dN/dS ratio (which measures the
+ relative excess of non-synonymous to synonymous polymorphism) and the
+ signature of recombination is detected from the patterns of linkage
+ disequilibrium. The model and the method of estimation are described
+ in
+ Wilson, D. J. and G. McVean (2006)
+ Estimating diversifying selection and functional constraint in the
+ presence of recombination.
+ Genetics doi:10.1534/genetics.105.044917.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: paml
+Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Phylogenetic Analysis by Maximum Likelihood
+ PAML is a package of programs for phylogenetic analyses of DNA or
+ protein sequences using maximum likelihood. It is maintained and
+ distributed for academic use free of charge by Ziheng Yang. ANSI C
+ source codes are distributed for UNIX/Linux/Mac OSX, and executables
+ are provided for MS Windows. PAML is not good for tree making. It may
+ be used to estimate parameters and test hypotheses to study the
+ evolutionary process, when you have reconstructed trees using other
+ programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: partigene
+Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: generating partial gemomes
+ PartiGene is part of the Edinburgh-EGTDC developed EST-software
+ pipeline at the moment consisting of trace2dbEST, PartiGene,
+ wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven,
+ multi-step software tool which takes sequences (usually ESTs) and
+ creates a dataabase of a non-redundant set of sequence objects
+ (putative genes) which we term a partial genome.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: pfaat
+Homepage: http://pfaat.sourceforge.net/
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Protein Family Alignment Annotation Tool
+ Pfaat is a Java application that allows one to edit, analyze, and
+ annotate multiple sequence alignments. The annotation features are a
+ key component as they provide a framework to for further sequence,
+ structure and statistical analysis.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: pftools
+Homepage: http://www.isrec.isb-sib.ch/profile/profile.html
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: handle profiles of protein domains
+ The 'pftools' package is a collection of experimental programs
+ supporting the generalized profile format and search method of
+ PROSITE.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: prank
+Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
+License: GPL (except two algorithms)
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
+ PRANK is a probabilistic multiple alignment program for DNA, codon
+ and amino-acid sequences. It's based on a novel algorithm that treats
+ insertions correctly and avoids over-estimation of the number of
+ deletion events. In addition, PRANK borrows ideas from maximum
+ likelihood methods used in phylogenetics and correctly takes into
+ account the evolutionary distances between sequences. Lastly, PRANK
+ allows for defining a potential structure for sequences to be aligned
+ and then, simultaneously with the alignment, predicts the locations
+ of structural units in the sequences.
+ .
+ PRANK is a command-line program for Unix-style environments but the
+ same sequence alignment engine is implemented in the graphical
+ program PRANKSTER. In addition to providing a user-friendly interface
+ to those not familiar with Unix systems, PRANKSTER is an alignment
+ browser for alignments saved in the HSAML format. The novel format
+ allows for storing all the information generated by the aligner and
+ the alignment browser is a convenient way to analyse and manipulate
+ the data.
+ .
+ PRANK aims at an evolutionarily correct sequence alignment and often
+ the result looks different from ones generated with other alignment
+ methods. There are, however, cases where the different look is caused
+ by violations of the method's assumptions. To understand why things
+ may go wrong and how to avoid that, read this explanation of
+ differences between PRANK and traditional progressive alignment
+ methods.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Comment: priam
+ BioLinux contains a priam package which is available at
+ http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this
+ project has only a "free as in beer" binary download - so this is not
+ for us ...
+
+Depends: prot4est
+Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: EST protein translation suite
+ prot4EST is a perl script that takes expressed sequence tags (ESTs)
+ and translates them optimally to produce putative peptides. prot4EST
+ intergrates a number of programs to overcome problems inherent with
+ translating ESTs.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: qtlcart
+Homepage: http://statgen.ncsu.edu/qtlcart/
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: map quantitative traits using a map of molecular markers
+ QTL Cartographer is a suite of programs to map quantitative traits
+ using a map of molecular markers. It contains a set of programs that
+ will aid in locating the genes that control quantitative traits using
+ a molecular map of markers. It includes some programs to allow
+ simulation studies of experiments.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: rbs-finder
+Homepage: http://www.genomics.jhu.edu/RBSfinder/
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: find ribosome binding sites(RBS)
+ The program implements an algorithm to find ribosome binding
+ sites(RBS) in the upstream regions of the genes annotated by
+ Glimmer2, GeneMark, or other prokaryotic gene finders. If there is
+ no RBS-like patterns in this region, program searches for a start
+ codon having a RBS-like pattern ,in the same reading frame upstream
+ or downstream and relocates start codon accordingly.
+ .
+ You can find more detailed information at
+ http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: recombine
+Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: effective population size of populations
+ RECOMBINE fits a model which has a single population of constant size
+ with a single recombination rate across all sites. It can accomodate
+ either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism)
+ data. It estimates 4Nu and r, where N is the effective population
+ size, u is the neutral mutation rate per site, and r is the ratio of
+ the per-site recombination rate to the per-site mutation rate.
+Remark: This software might be outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting RECOMBINE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however." So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Depends: splitstree
+Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Analyzing and Visualizing Evolutionary Data
+ Evolutionary data is most often presented as a phylogentic tree, the
+ underlying assumption being that evolution is a branching
+ process. However, real data is never ideal and thus doesn't always
+ support a unique tree, but often supports more than one possible
+ tree. Hence, it makes sense to consider tree reconstruction methods
+ that produce a tree, if the given data heavily favors one tree over
+ all others, but otherwise produces a more general graph that
+ indicates different possible phylogenies. One such method is the
+ Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
+ Dress (1992) and its variations. Another example is Spectral Analysis
+ developed by Hendy, Penny and others.
+ .
+ These and other methods are implemented in the program SplitsTree,
+ that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
+ Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
+ format.
+ .
+ Note: There is a new version 4.0 written from scratch at
+ http://www.splitstree.org/ which requires a license key - so this is
+ probably non-free. Version 3.2 which is linked above has some
+ downloadable source code without any license or copyright statement -
+ so it has to be clarified whether we are able to distribute this code
+ or not.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+
+Depends: taverna
+Homepage: http://taverna.sourceforge.net/
+License: LGPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: designing and executing myGrid workflows for bioinformatics
+ The Taverna workbench is a free software tool for designing and
+ executing workflows, created by the myGrid project, and funded
+ through OMII-UK. Taverna allows users to integrate many different
+ software tools, including web services, such as those provided by the
+ National Center for Biotechnology Information, The European
+ Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab,
+ BioMOBY and EMBOSS.
+ .
+ The Taverna Workbench provides a desktop authoring environment and
+ enactment engine for scientific workflows expressed in Scufl (Simple
+ Conceptual Unified Flow language). The Taverna enactment engine is
+ also available separately, and other Scufl enactors are available
+ including Moteur. The myExperiment social web site supports finding
+ and sharing of workflows and has special support for Scufl
+ workflows. The Taverna workbench, myExperiment and associated
+ components are developed and maintained by the myGrid team, in
+ collaboration with the open source community.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: taxinspector
+Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
+License: Artistic + other free licenses
+Responsible: BioLinux - Tim Booth <tbooth at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: browser for entries in the NCBI taxonomy
+ TaxInspector is a browser for entries in the NCBI taxonomy. It is
+ designed to run as a plugin to annotation software such as maxdLoad2
+ and Pedro, but also has a standalone mode.
+Remark: This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: tetra
+Homepage: http://www.megx.net/tetra/
+License: free academic
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: tetranucleotide frequency calculator
+ The TETRA program can be used to calculate how well tetranucleotide
+ usage patterns in DNA sequences correlate. Such correlations can
+ provide valuable hints on the relatedne ss of DNA sequences, and are
+ particularly useful for metagenomic sequences.
+Remark: for the Linux version
+ Version 1.0.2 (Mac OSX has version
+ 2.0b30) is deprecated and hence a feature-limited version of
+ TETRA. At the time writing, no decisions have been made about
+ adapting and cross-compiling the Mac OS X code for this platform. A
+ Linux version might happen when REALbasic's Linux IDE is more mature.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: trace2dbest
+Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: process trace files into dbEST submissions
+ Trace2dbest is part of the PartiGene pipeline.
+ .
+ Trace2dbest takes a series of sequence traces and converts them into
+ basecalled files. It also creates files in the appropriate format for
+ submission to dbEST and allows you to submit them directly if your
+ machine is configured to allow mailing to external sites. The output
+ from trace2dbest can be used as input to the PartiGene program.
+ .
+ Trace2dbEST process raw sequenceing chromatograph trace files from
+ EST projects into quality-checked sequences, ready for submission to
+ dbEST. trace2dbEST guides you through the creation of all the
+ necessary files for submission of ESTs to dbEST. trace2dbest makes
+ use of other software (available free under academic licence) that
+ you will need to have installed, namely phred, cross_match and
+ (optionaly) BLAST.
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: profit
+Homepage: http://www.bioinf.org.uk/software/profit/
+License: non-free
+Responsible: Steffen Moeller <steffen_moeller at gmx.de>
+WNPP: 525428
+Pkg-Description: structural alignment of multiple proteins
+ ProFit is designed to be the ultimate protein least squares fitting
+ program. It has many features including flexible specification of
+ fitting zones and atoms, calculation of RMS over different zones or
+ atoms, RMS-by-residue calculation, on-line help facility, etc.
+Remark: The authors need to change the license, still.
+ The debian folder should appear in Debian Med Svn in some near future.
+
+Depends: kempbasu
+Homepage: http://code.google.com/p/kempbasu/
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kempbasu/trunk/
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: Significance tests for comparing digital gene expression profiles
+ This package implements the significance tests for comparing digital
+ gene profiles described in the article:
+ .
+ Varuzza _et al_. *"Significance tests for comparing digital gene
+ expression profiles"*
+ .
+ They provide two programs: kemp for the frequentist test and basu for
+ the Bayesian test, and some auxiliary scripts.
+
+Depends: fastx-toolkit
+Homepage: http://hannonlab.cshl.edu/fastx_toolkit
+License: AGPL / MIT
+Responsible: Assaf Gordon <gordon at cshl.edu>
+Pkg-Description: collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
+ Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple
+ short-reads sequences (possibly with quality information). The main processing of such
+ FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other
+ databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP,
+ LastZ, MAQ and many many others.
+ .
+ However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the
+ sequences to the genome - manipulating the sequences to produce better mapping results.
+ .
+ The FASTX-Toolkit tools perform some of these preprocessing tasks.
+Remark: See also
+ http://hannonlab.cshl.edu/column_normalizer/
+ .
+ http://hannonlab.cshl.edu/crosstab/
+
+Depends: grogui
+Homepage: http://www.kde-apps.org/content/show.php?content=47665
+License: GPL
+Pkg-Description: graphical user interface for popular molecular dynamics package GROMACS
+ 1. File browsing and management with customizable right-click pop up menu.
+ 2. Graphical interfaces for GROMACS commands (currently 21 commands have their own interfaces).
+ 3. Plot drawing tool which can export plots to pdf.
+ 4. A simple built-in console.
+ 5. Built-in GROMACS manual viewer.
+ 6. Built-in file editor with syntax highlighting for some GROMACS file formats (currently only mdp format is supported).
+ 7. MDP Writer section to easily create your mdp files.
+ 8. File icons based on their types.
+
+Depends: rosetta
+Homepage: http://www.rosettacommons.org/
+License: not redistributable, not unlikely to change
+Pkg-Description: Protein-folding, -docking, ..?
+ Rosetta is a much renowned tool for the molecular modelling of protein
+ structures, small chemical, and interactions between any of these.
+ It is developed by a consortium of several american academic research
+ groups. Industry can by licenses from a not-for-profit company, while
+ academic groups have the opportunity to download the source and build
+ it locally. That license explicitly denies the right to redistribute
+ the source or binaries. Nevertheless, Debian-Med could possibly offer
+ an easy preparation of Debian packages.
+
+Depends: obo-edit
+Homepage: http://www.geneontology.org
+License: something free
+Pkg-Description: editor for biological ontologies
+ (Open Biological Ontologies) Obo-Edit supports the formal representation
+ of biological entities and the specification of is-a (specialisation)
+ and part-of relations. Amongst the databases cureated by this tool
+ is the GeneOntology.
+
+Suggests: pdb2pqr
Added: projects/med/tags/1.3/tasks/bio-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/bio-dev?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/bio-dev (added)
+++ projects/med/tags/1.3/tasks/bio-dev Sat Jun 23 12:46:46 2012
@@ -1,0 +1,207 @@
+Task: Biology Development
+Description: Debian Med packages for development of micro-biology applications
+ This metapackage will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
+Depends: bioperl, bioperl-run, libncbi6-dev, mcl
+
+Comment: biomode is removed from Debian because it is orphaned upstream, outdated
+ and doese not work with recent Emacs any more
+
+Depends: libvibrant6-dev
+Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install
+ libmotif-dev it must be possible to deinstall libvibrant6-dev without
+ beeing forced to deinstall med-bio-dev as well
+
+Depends: python-biopython
+
+Depends: libbio-ruby
+
+Depends: libbiojava-java
+
+Depends: libqsearch-dev
+
+Depends: libgenome-1.3-0-dev
+
+Depends: libbio-mage-perl
+Why: Useful for the submission of microarray data to public repositories.
+
+Depends: libajax5-dev, libnucleus5-dev
+
+Depends: libtfbs-perl
+
+Depends: libgo-perl
+
+Depends: r-cran-genetics, r-cran-haplo.stats
+
+Depends: octave-bioinfo
+
+Depends: libbio-graphics-perl
+
+Depends: libbio-primerdesigner-perl
+
+Depends: libace-perl
+
+Depends: libbiococoa-dev
+
+Depends: libstaden-read-dev
+
+Suggests: r-cran-rocr
+Why: Even if this package is not directly connected to biology it is maintained by
+ Debian Med team and should be in our focus and it is not wrong to suggest this
+ package for development of biological applications based on R
+
+Depends: bioconductor
+Homepage: http://www.bioconductor.org/
+Responsible: Debian CRAN/BioConductor/Omegahat packaging team <pkg-bioc-devel at lists.alioth.debian.org>
+License: GPL/LGPL
+Pkg-URL: http://wiki.debian.org/AliothPkgBioc
+Pkg-Description: analysis and comprehension of genomic data
+ Bioconductor is an open source and open development software project
+ to provide tools for the analysis and comprehension of genomic data.
+ .
+ The Bioconductor core team is based primarily at the Biostatistics Unit of
+ the Dana Farber Cancer Institute at the Harvard Medical School/Harvard School
+ of Public Health. Other members come from various US and international
+ institutions.
+ .
+ The broad goals of the projects are to
+ * provide access to a wide range of powerful statistical and graphical methods
+ for the analysis of genomic data;
+ * facilitate the integration of biological metadata in the analysis of
+ experimental data: e.g. literature data from PubMed, annotation data from
+ LocusLink;
+ * allow the rapid development of extensible, scalable, and interoperable
+ software;
+ * promote high-quality documentation and reproducible research;
+ * provide training in computational and statistical methods for the analysis
+ of genomic data.
+ .
+ A nice overview about all modules of BioDonductor is given at
+ http://www.bioconductor.org/packages/release/bioc/
+
+Depends: bioclipse
+Homepage: http://www.bioclipse.net/
+License: Eclipse Public License (EPL) + exception
+Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
+ The Bioclipse project is aimed at creating a Java-based, open source,
+ visual platform for chemo- and bioinformatics based on the Eclipse
+ Rich Client Platform (RCP). Bioclipse, as any RCP application, is based
+ on a plugin architecture that inherits basic functionality and visual
+ interfaces from Eclipse, such as help system, software updates,
+ preferences, cross-platform deployment etc.
+ .
+ Bioclipse will provide functionality for chemo- and bioinformatics,
+ and extension points that easily can be extended by plugins to provide
+ added functionality. The first version of Bioclipse includes a
+ CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin
+ (bc_jmol) for 3D-visualization and a general logging plugin. To stay
+ updated on upcoming features, releases, new plugins etc, please register
+ for the mailing list bioclipse-announce. The development is best
+ followed on the Bioclipse Wiki where we document the progress and
+ ideas of the development on a daily basis.
+
+Depends: libgff-perl
+Homepage: http://www.sanger.ac.uk/Software/formats/GFF/
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL-1+
+WNPP: 468826
+Pkg-Description: Perl bindings for GFF Annotation Protocol
+ GFF (Gene Finding Feature) is a format for describing genes and other
+ features associated with DNA, RNA and Protein sequences.
+ .
+ This package provides a Perl module to use GFF objects.
+
+Depends: libmems-1.5-1
+Homepage: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmems.html
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Pkg-URL: http://people.debian.org/~tille/packages/libmems/
+Pkg-Description: library to support DNA string matching and comparative genomics
+ libMems is a freely available software development library to support DNA
+ string matching and comparative genomics. Among other things, libMems
+ implements an algorithm to perform approximate multi-MUM and multi-MEM
+ identification. The algorithm uses spaced seed patterns in conjunction
+ with a seed-and-extend style hashing method to identify matches. The method
+ is efficient, requiring a maximum of only 16 bytes per base of the largest
+ input sequence, and this data can be stored externally (i.e. on disk) to
+ further reduce memory requirements.
+
+Depends: libbio-das-perl
+Homepage: http://www.biodas.org/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: Perl Artistic License
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libbio-das-perl/trunk
+Pkg-Description: interface to Distributed Annotation System (DAS)
+ Bio::Das provides access to genome sequencing and annotation databases
+ that export their data in Distributed Annotation System (DAS) format
+ version 1.5. Both unencrypted (http:) and SSL-encrypted (https:)
+ DAS servers are supported.
+
+Depends: limma
+Homepage: http://bioinf.wehi.edu.au/limma
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 293320
+License: LGPL
+Pkg-Description: library for linear models and differential gene expression analysis
+ Limma is an essential package of the bioconductor.org effort to
+ investigate gene expression data from microarrays with the
+ statistical package R.
+
+Depends: libbio-mage-utils-perl
+Homepage: http://mged.sourceforge.net/
+License: MIT/X
+WNPP: 476202
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-URL: http://mentors.debian.net/debian/pool/main/l/libbio-mage-utils-perl/
+Pkg-Description: Extra modules for classes in the MAGE package: MAGE
+ MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the
+ Microarray Gene Expression Data Society (MGED). This package contains Perl
+ modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum
+ Information About a Microarray Experiment) records of microarray ("DNA chips")
+ experiments.
+ .
+ Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology,
+ as well as SQL utilities.
+
+Depends: seqan
+Homepage: http://www.seqan.de/
+License: LGPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seqan/trunk/
+WNPP: 487361
+Responsible: Soeren Sonnenburg <bugreports at nn7.de>
+Pkg-Description: C++ template library for the analysis of sequences.
+ SeqAn is a C++ template library of efficient algorithms and data
+ structures for the analysis of sequences with the focus on
+ biological data. This library applies a unique generic design that
+ guarantees high performance, generality, extensibility, and
+ integration with other libraries. SeqAn is easy to use and
+ simplifies the development of new software tools with a minimal loss
+ of performance.
+Remark: Recent development status of seqan
+ See http://lists.debian.org/debian-med/2009/06/msg00000.html for recent
+ discussion on Debian Med mailing list.
+
+Depends: libsbml1
+Homepage: http://www.sbml.org/
+License: LGPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libsbml/trunk/
+Responsible: Moriyoshi Koizumi <mozo at sfc.keio.ac.jp>
+Pkg-URL: http://www.e-cell.org/ecell/software/downloads
+Pkg-Description: System Biology Markup Language Library
+ LibSBML is a library designed to help you read, write, manipulate,
+ translate, and validate SBML files and data streams. It is not an
+ application itself (though it does come with many example programs),
+ but rather a library you can embed in your own applications.
+ .
+ LibSBML is written in ISO C and C++ but as a library it may be
+ used from all the programming languages listed to the left. In fact,
+ we strive to adhere to the natural idioms of each particular language
+ to make the libSBML programming experience seamless. For example, SBML
+ <listOf> elements behave like lists and sequences in Python, but
+ vectors in Matlab. Also, the C and C++ interfaces are completely
+ distinct (it's possible to program in pure C), but in C++ the C APIs
+ may be called without sacrifcing type safety.
+ .
+ The LibSBML code is very portable and is supported on Linux, Windows
+ (native), and Mac OS X.
Added: projects/med/tags/1.3/tasks/cms
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/cms?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/cms (added)
+++ projects/med/tags/1.3/tasks/cms Sat Jun 23 12:46:46 2012
@@ -1,0 +1,6 @@
+Task: Content Management
+Description: Debian Med content management systems
+ This metapackage will install packages which are useful to build a
+ content management system for medical care.
+
+Suggests: zope-zms
Added: projects/med/tags/1.3/tasks/data
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/data?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/data (added)
+++ projects/med/tags/1.3/tasks/data Sat Jun 23 12:46:46 2012
@@ -1,0 +1,30 @@
+Task: Medical data
+Description: Debian Med suggestions for medical databases
+ Currently Debian Med does not yet contain any medical data like drug
+ databases. We just provide a list of Free Software that might be used
+ and which might be included into Debian at a later point in time
+ provided somebody is willing to take over the packaging work.
+
+Depends: drugref.org
+Homepage: http://savannah.nongnu.org/projects/php-drugref/
+License: GPL2+
+Pkg-Description: pharmaceutical reference database
+ Important note: The project seems to be dead and the domain drugref.org
+ does not exist any more. Thanks to the GNU Savannah project the code was
+ kept for the past but there is no guarantee at all that the project is
+ of any use.
+ .
+ The aim to to allow the collaborative construction of a free,
+ peer-reviewed pharmaceutical reference.
+ .
+ The primary motivation is to support the gnumed project -- a free software
+ medical information system, but it may have other uses.
+ .
+ It will support logging and versioning of all data, changes made by
+ contributors can be audited and reverted if necessary. The data can
+ be peer-reviewed by several authorities, end-users can opt to have
+ only data which is peer-reviewed.
+ .
+ Drug names, indications, interactions, contra-indications, adverse
+ reactions and side-effects are supported. Product information for
+ multiple countries can be entered.
Added: projects/med/tags/1.3/tasks/epi
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/epi?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/epi (added)
+++ projects/med/tags/1.3/tasks/epi Sat Jun 23 12:46:46 2012
@@ -1,0 +1,89 @@
+Task: Epidemiology
+Description: Debian Med epidemiology related packages
+ This metapackage will install tools that are useful in epidemiological
+ research. Several packages making use of the GNU R data language for
+ statistical investigation. It might be a good idea to read the paper
+ "A short introduction to R for Epidemiology" at
+ http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
+
+Depends: epigrass
+
+Suggests: r-cran-msm
+
+Depends: r-cran-epibasix
+
+Depends: r-cran-epitools
+X-Comment: See also: http://sites.google.com/site/medepi/epitools
+
+Depends: r-cran-surveillance
+
+Depends: r-cran-epi
+
+Depends: netepi-analysis
+Homepage: http://sourceforge.net/projects/netepi
+Responsible: Andreas Tille <tille at debian.org>
+License: MPL 1.1
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/netepi-analysis/trunk
+Pkg-Description: network-enabled tools for epidemiology and public health practice
+ NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative
+ project to create a suite of free, open source software tools for epidemiology
+ and public health practice. Anyone with an interest in population health
+ epidemiology or public health informatics is encouraged to examine the prototype
+ tools and to consider contributing to their further development. Contributions
+ which involve formal and/or informal testing of the tools in a wide range of
+ circumstances and environments are particularly welcome, as is assistance with
+ design, programming and documentation tasks.
+ .
+ This is a tool for conducting epidemiological analysis of data sets, both large
+ and small, either through a Web browser interface, or via a programmatic
+ interface. In many respects it is similar to the analysis facilities included
+ in the Epi Info suite, except that NetEpi Analysis is designed to be installed
+ on servers and accessed remotely via Web browsers, although it can also be
+ installed on individual desktop or laptop computers.
+ .
+ The software was developed by New South Wales Department of Health.
+ .
+ There is also a Google code project page at http://code.google.com/p/netepi/
+ .
+ See also: http://www.stockholmchallenge.se/data/2123 and
+ http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
+
+Depends: netepi-collection
+Homepage: http://sourceforge.net/projects/netepi
+Responsible: Andreas Tille <tille at debian.org>
+License: MPL 1.1
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/netepi-collection/trunk
+Pkg-Description: network-enabled tools for epidemiology and public health practice
+ NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative
+ project to create a suite of free, open source software tools for epidemiology
+ and public health practice. Anyone with an interest in population health
+ epidemiology or public health informatics is encouraged to examine the prototype
+ tools and to consider contributing to their further development. Contributions
+ which involve formal and/or informal testing of the tools in a wide range of
+ circumstances and environments are particularly welcome, as is assistance with
+ design, programming and documentation tasks.
+ .
+ NetEpi Case Manager is a tool for securely collecting structured
+ information about cases and contacts of communicable (and other)
+ diseases through Web browsers and the Internet. New data collection
+ forms can be designed and deployed quickly by epidemiologists, using a
+ "point-and-click" interface, without the need for knowledge of or
+ training in any programming language. Data can then be collected from
+ users of the system, who can be located anywhere in the world, into a
+ centralised database. All that is needed by users of the system is a
+ relatively recent Web browser and an Internet connection ("NetEpi"
+ is short for "Network-enabled Epidemiology"). In many respects,
+ NetEpi Case Manager is like a Web-enabled version of the data entry
+ facilities in the very popular Epi Info suite of programmes published by
+ the US Centers for Disease Control and Prevention, and in the Danish
+ EpiData project, which is available for several languages. The software
+ was developed by the Centre for Epidemiology and Research of the New
+ South Wales Department of Health, with contributions from Population
+ Health Division of the Australian Government Department of Health and
+ Ageing.
+ .
+ The software was developed by New South Wales Department of Health.
+ .
+ See also: http://www.stockholmchallenge.se/data/2123 and
+ http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf
+
Added: projects/med/tags/1.3/tasks/his
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/his?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/his (added)
+++ projects/med/tags/1.3/tasks/his Sat Jun 23 12:46:46 2012
@@ -1,0 +1,126 @@
+Task: Hospital Information Systems
+Description: Debian Med suggestions for Hospital Information Systems
+ Currently Debian Med does not yet contain any software which can be
+ regarded as Hospital Information System. There is some Free Software
+ out there which might be interesting targets for inclusion into Debian
+ and so we provide a list of these projects which might be included
+ at a later point in time provided somebody is willing to take over
+ the packaging work.
+
+Depends: medical
+Homepage: http://medical.sourceforge.net/
+License: GPL
+Pkg-Description: centralized Electronic Medical Record and Hospital Information System
+ Medical is a multi-user, highly scalable, centralized Electronic Medical Record (EMR)
+ and Hospital Information System (HIS) for openERP, so doctors and institutions all over
+ the world, independently of their economic status, will benefit from a centralized,
+ high quality, secure and scalable system.
+ .
+ Medical at a glance:
+ * 100% paperless patient examination and history taking
+ * Patient Administration (creation, evaluations / consultations, history ... )
+ * Strong focus in family medicine and Primary Health Care
+ * Doctor Administration
+ * Lab Administration
+ * Medicine / Drugs information (vademécum)
+ * Medical stock and supply chain management
+ * Demographics and other statistical reports
+ * Financial Administration (Invoicing, ...).
+ * Designed with industry standards in mind
+
+Depends: care2x
+Homepage: http://sourceforge.net/projects/care2002/
+License: GPL / LGPL
+Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=53886&package_id=133412
+Pkg-Description: Integrated Hospital Information System
+ Functions: surgery, nursing, outpatient, wards, labs, security, admission,
+ schedulers, repair, communication & more. Multilanguage, userconfig,
+ embedded AI & work bots. Modular & scalable.
+ .
+ Official Homepage http://www.care2x.org/ seems to have some problems from time to
+ time.
+ .
+ Inoffical Debian package of alpha version:
+ http://downloads.sourceforge.net/care2002/care2x-2.6.alpha.deb?use_mirror=mesh
+
+Depends: fis-gtm
+Homepage: http://fis-gtm.com
+License: AGPL v3
+WNPP: 541239
+Responsible: K.S. Bhaskar <ks.bhaskar at fnis.com>
+Pkg-Description: Database Engine with Extreme Scalability and Robustness
+ GT.M is a database engine with scalability proven in large real-time
+ transaction processing systems that have thousands of concurrent
+ users, individual database file sizes to the Terabyte range (with
+ virtually unlimited aggregate database sizes). Yet the light
+ footprint of GT.M allows it to also scale down for use in small
+ applications and software appliances (virtual machines).
+ .
+ The GT.M data model is hierarchical associative memory (i.e.,
+ multi-dimensional array) that imposes no restrictions on the data
+ types of the indexes or content - the application logic can impose
+ any schema, dictionary or data organization suited to its problem
+ domain. (Database engines that do not impose schemas, but which
+ allow layered application software to impose and use whatever schema
+ that is appropriate to the application are popularly referred to as
+ "document oriented", "schemaless" or "schema-free" databases.)
+ .
+ GT.M's compiler for the standard M (also known as MUMPS) scripting
+ language implements full support for ACID (Atomic, Consistent,
+ Isolated, Durable) transactions, using optimistic concurrency control
+ and software transactional memory (STM) that resolves the common
+ mismatch between databases and programming languages. Its unique
+ ability to create and deploy logical multi-site configurations of
+ applications provides unrivaled continuity of business in the face of
+ not just unplanned events, but also planned events, including planned
+ events that include changes to application logic and schema.
+ .
+ Community support forums for GT.M can be found at
+ http://sourceforge.net/projects/fis-gtm and support with assured
+ service levels on commercial terms can be purchased from
+ gtmsupport at fnis.com.
+
+Depends: vista
+Homepage: http://worldvista.org/AboutVistA
+License: Public Domain, GPL v2, AGPL v3
+WNPP: 541242
+Responsible: K.S. Bhaskar <ks.bhaskar at fnis.com>
+Pkg-Description: Real time health care information system including electronic health record
+ VistA is the complete health care information system (HIS) which
+ is developed and used by the US Department of Veterans Affairs to
+ run all of its hospitals and clinics. It is in the public domain
+ through the US Freedom of Information Act. Versions are also in
+ use both in the US and internationally, including the US Department
+ of Defense, the US Indian Health Service, the Mexican Instituto
+ Mexicano del Seguro Social, etc. There are also flavors of VistA
+ provided by WorldVistA (http://worldvista.org) and Medsphere
+ (http://medsphere.org).
+
+Depends: world-vista
+Homepage: http://worldvista.org/World_VistA_EHR
+License: GPL v2
+Responsible: K.S. Bhaskar <ks.bhaskar at fnis.com>
+WNPP: 541245
+Pkg-Description: repackage and extended version of VistA produced by WorldVistA
+ Developed by WorldVistA (http://worldvista.org) and released under GPL
+ v2, WorldVistA EHR is a repackaged and extended version of the VistA
+ health care information system (HIS) developed by the US Department of
+ Veterans Affairs, and in the public domain through the US Freedom of
+ Information Act.
+ .
+ WorldVistA successfully submitted WorldVistA EHR for certification by
+ CCHIT (http://cchit.org) in 2007. WorldVistA EHR VOE/ 1.0 was tested
+ and passed inspection of 100 percent of a set of criteria for
+ functionality (ability to create and manage electronic records for all
+ patients, as well as automating workflow in a physician's office),
+ interoperability (a first step in the ability to receive and send
+ electronic data to other entities such as laboratories), and security
+ (ability to keep patients' information safe).
+
+Depends: ipath
+Homepage: http://ipath.sourceforge.net/
+License: GPL
+Pkg-Description: telemedicine platform
+ iPath is an open source platform for telemedicine applications such as consulations,
+ case disucssions, virtual staff meetings, etc. It was originally developed at University
+ of Basel where a public iPath server for projects with developing countries is hosted.
Added: projects/med/tags/1.3/tasks/imaging
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/imaging?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/imaging (added)
+++ projects/med/tags/1.3/tasks/imaging Sat Jun 23 12:46:46 2012
@@ -1,0 +1,602 @@
+Task: Imaging
+Description: Debian Med imaging packages
+ This metapackage will install Debian packages which might be useful in
+ medical image processing.
+ .
+ It installs several packages supporting DICOM (Digital Imaging and
+ Communications in Medicine) which is the de-facto standard for medical
+ image management. The standard defines data structures and services for
+ the exchange of medical images and related information. The latest release
+ has been published in 2008 and consists of 18 parts.
+ .
+ For more information, you can visit the NEMA homepage
+ http://medical.nema.org/ .
+ .
+ The status of the official DICOM base standard plus all the
+ supplements and correction items are summarized at David Clunie's webpage:
+ http://www.dclunie.com/dicom-status/status.html
+ where you'll find direct links to the most recent yearly edition
+ ftp://medical.nema.org/medical/dicom/2008/ .
+
+Depends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nifti, xmedcon, dcmtk
+
+Suggests: imagemagick, pngquant, imview
+
+Depends: nifti-bin
+
+Depends: aeskulap
+
+Depends: fslview, fsl
+
+Depends: gwyddion
+
+Depends: sofa-apps
+
+Depends: python-mvpa
+Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
+
+Depends: python-nipy
+Why: Although listed in -dev task, it also has a strong focus on interactive
+ data analysis.
+
+Depends: caret
+
+Depends: libgdcm-tools
+
+Depends: slicer
+
+Depends: bioimagesuite
+Homepage: http://www.bioimagesuite.org/
+License: GPL
+Pkg-Description: integrated image analysis software suite
+ BioImage Suite has extensive capabilities for both neuro/cardiac
+ and abdominal image analysis and state of the art visualization.
+ Many packages are available that are highly extensible, and provide
+ functionality for image visualization and registration, surface
+ editing, cardiac 4D multi-slice editing, diffusion tensor image
+ processing, mouse segmentation and registration, and much more. It
+ can be intergrated with other biomedical image processing software,
+ such as FSL and SPM. This site provides information, downloads,
+ documentation, and other resources for users of the software.
+ .
+ BioImage Suite was developed at Yale University and has been
+ extensively used at different labs at Yale since 2004.
+ .
+ There is a forum at BioImage Suite site for discussion of
+ compiling it from source and packaging issues at
+ http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0
+
+Depends: drjekyll
+Homepage: http://drjekyll.sourceforge.net
+License: GPL
+Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images
+ It is specifically aimed at postprocessing of segmented datasets,
+ but offers some functionality for raw data as well.
+ Voxel elements (=voxels) and pixel ("picture element") are viewed
+ as data sets and can be processed by this program as kind of
+ a final polishing process.
+Why: Hint given by Petter Reinholdtsen
+
+Depends: libvista2
+Homepage: http://mia.sourceforge.net/
+License: GPL
+Pkg-Description: software environment for computer vision research
+ Vista is a software environment for computer vision research. It is
+ designed to support not only images, but also edge sets, camera models,
+ and more complex data structures. Vista includes libraries of common
+ computer vision and image processing algorithms. It is written in
+ ANSI C, for UNIX platforms running X Windows, and it is freely available.
+ The original development was done at University of British Columbia
+ (http://www.cs.ubc.ca/nest/lci/vista/vista.html).
+ .
+ Because the development was stalled by the original authors the
+ development continued in the "Tools for Medical Image Analysis"
+ framework (http://mia.sourceforge.net/) which is maintained by
+ Max Planck Institute of Cognitive Neuroscience
+ (http://www.cns.mpg.de/).
+
+Depends: dcm4che
+Homepage: http://www.dcm4che.org/
+License: LGPL, MPL, Apache, other (also non-free)
+Pkg-Description: collection of open source applications and utilities healthcare enterprise
+ At the core of the dcm4che project is a robust implementation of the
+ DICOM standard. The dcm4che-1.x DICOM toolkit is used in many production
+ applications across the world, while the current (2.x) version of the
+ toolkit has been re-architected for high performance and flexibility.
+ .
+ Also contained within the dcm4che project is dcm4chee (the extra 'e'
+ stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive
+ (according to IHE). The application contains the DICOM, HL7 services
+ and interfaces that are required to provide storage, retrieval, and
+ workflow to a healthcare environment. dcm4chee is pre-packaged and
+ deployed within the JBoss application server. By taking advantage of
+ many JBoss features (JMS, EJB, Servlet Engine, etc.), and assuming the
+ role of several IHE actors for the sake of interoperability, the
+ application provides many robust and scalable services.
+
+
+Depends: piano
+Homepage: http://mbi.dkfz-heidelberg.de/mbi/software/
+License: BSD
+Pkg-Description: medical image processing library for surgical planning
+ Piano is a library containing roughly 75 algorithms and tools for
+ multi-dimensional medical image processing, analysis and visualization.
+ It is used in the field of surgical planning.
+
+Depends: pixelmed
+Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
+License: Free
+Pkg-Description: PixelMed Java DICOM Toolkit
+ This is a stand-alone DICOM toolkit that implements code for reading and
+ creating DICOM data, DICOM network and file support, a database of DICOM objects,
+ support for display of directories, images, reports and spectra, and DICOM object
+ validation.
+
+Depends: mesa-test-tools
+Homepage: http://ihedoc.wustl.edu/mesasoftware/
+License: free
+Pkg-Description: IHE Test Software for Radiology
+ The MESA software release which is available at
+ http://ihedoc.wustl.edu/mesasoftware/10.15.0/dist/ provides several
+ tools that might cover a wide range of applications for
+ Integrating the Healthcare Enterprise (IHE) testing.
+ .
+ Another important element of the IHE testing process is the set of
+ software tools HIMSS and RSNA have commissioned. Developed by the
+ Electronic Radiology Laboratory at the Mallinckrodt Institute of
+ Radiology, Washington University of St. Louis, the MESA tools are
+ designed for use by participating companies in implementing IHE
+ capabilities in their systems and preparing for the Connectathon. Their
+ purpose is to provide communication partners, test data and test plans
+ to allow organizations to provide a baseline level of testing as they
+ implement the IHE Technical Framework. These tools are made available to
+ participants during the period of an IHE demonstration year and are then
+ released into the public domain at the end of that cycle. The latest
+ version of the MESA Test Tools available in the public domain can be
+ found here.
+ .
+ This kind of software is definitively valuable for information systems
+ vendors and imaging systems vendors.
+ .
+ Because the CTN Debian package is based on an upstream dead project
+ these tools should have a high priority for packaging because the
+ CTN homepage http://erl.wustl.edu/research/dicom/ctn.html says:
+ "The CTN software is also embedded within the MESA tools. The version
+ of CTN software in those tools does not have a separate release number
+ but is more current than version 3.0.6."
+
+Depends: devide
+Homepage: http://code.google.com/p/devide/
+License: BSD
+WNPP: 509110
+Responsible: Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Pkg-Description: Delft Visualization and Image processing Development Environment
+ DeVIDE, or the Delft Visualization and Image processing Development
+ Environment, is a Python-based dataflow application builder that enables
+ the rapid prototyping of medical visualization and image processing
+ applications via visual programming. In other words, by visually connecting
+ functional blocks (think Yahoo pipes), you can create cool visualizations.
+ .
+ See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE
+
+Depends: dicom4j
+Homepage: http://dicom4j.sourceforge.net/
+License: GPL
+Pkg-Description: Java framework for Dicom
+ Java framework for Dicom
+
+Depends: opendicom.net
+Homepage: http://opendicom.sourceforge.net/
+License: LGPL
+Responsible: Albert Gnandt <agnandt at users.sourceforge.net>
+Pkg-URL: http://ubuntu.mi.hs-heilbronn.de/other/opendicom
+Pkg-Description: API to DICOM in C# for Mono
+ The openDICOM.NET project implements a new approach towards DICOM
+ (Digital Imaging and Communications in Medicine) libraries. DICOM is
+ a worldwide standard in Medical IT and is provided by the National
+ Electrical Manufacturers Assocation (NEMA). This standard specifies
+ the way medical images and meta data like study or patient related
+ data is stored and communicated over different digital medias. Thus,
+ DICOM is a binary protocol and data format.
+ .
+ The openDICOM# Class Libary, main part of the openDICOM.NET project,
+ provides an API to DICOM in C# for Mono and the .NET Framework. It is
+ a completely new implementation of DICOM. In contrast to other
+ similar libraries the intention of this implementation is to provide
+ a clean classification with support of unidirectional DICOM data
+ streaming. Another implemented goal is the support of DICOM as
+ XML. This is not standard conform but very use- and powerful within
+ software development, storage and manipulation. Currently, full read
+ support of DICOM output stream and full write support to XML is
+ supposed to be provided. The entire DICOM content can be accessed as
+ sequence or as tree of class instances. Latter is the default
+ representation of DICOM content by the library.
+ .
+ The openDICOM.NET Utils are a collection of console tools for working
+ with the needed data dictionaries in different data formats (binary
+ and textual), query of ACR-NEMA (prior DICOM standard) and DICOM
+ files and transcoding them into image formats like JPEG and XML
+ files. These utils are written in C# for Mono and the .NET Framework
+ and are using the openDICOM# API for processing.
+ .
+ The openDICOM.NET Navigator recapitulates the openDICOM.NET Utils in
+ form of a GTK# GUI. It provides different views with focus on DICOM
+ data sets and visualization. Connectivity to GIMP is also given for
+ single image processing purpose as well as the possibility to run
+ through multi-frame images like a movie.
+ .
+ The openDICOM.NET Beagle Filter Plugin increases the usability of
+ ACR-NEMA and DICOM query within your desktop. It makes DICOM content
+ overall indexable for retrieval. The Beagle search engine relies on
+ Mono/.NET and works in the background of your system, but is able to
+ detect content changes in realtime (depending on your configuration).
+ .
+ All GUI applications focus the popular GNOME desktop, but are 100%
+ platform independent by relying on Mono.
+
+Depends: afni
+Homepage: http://afni.nimh.nih.gov/
+WNPP: 409849
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+License: GPL
+Pkg-URL: http://sourceforge.net/project/showfiles.php?group_id=61662&package_id=60298
+Pkg-Description: environment for processing and displaying functional MRI data
+ AFNI is an environment for processing and displaying functional
+ MRI data. It provides a complete analysis toolchain, including
+ 3D cortical surface models, and mapping of volumetric data (SUMA).
+ In addition to its own format AFNI understands the NIfTI format and is
+ therefore easily usable in combination with FSL and Freesurfer.
+
+Depends: blox
+Homepage: http://sourceforge.net/projects/blox/
+License: GPL
+Pkg-Description: medical imaging and visualization program
+ The purpose of the project is to develop a quantitative medical
+ imaging and visualization program for use on brain MR, DTI and MRS
+ data. It is a joint project of the Kennedy Krieger Institute and the
+ Johns Hopkins University, Psychiatric Neuroimaging Lab
+ (http://pni.med.jhu.edu/methods/morph.htm).
+
+Depends: conquest-dicom-server
+Homepage: http://www.xs4all.nl/~ingenium/dicom.html
+License: Public domain
+Pkg-Description: full featured DICOM server
+ A full featured DICOM server that has been developed based on and
+ heavily extending the public domain UCDMC DICOM code.
+ Some possible applications of the Conquest DICOM software are:
+ * DICOM training and testing
+ * Demonstration and research image archives
+ * Image format conversion from a scanner with DICOM network access
+ * DICOM image viewing and slide making
+ * DICOM image selection, (limited) editing, and splitting and merging of series
+ * Advanced automatic image forwarding and (de)compression
+ * DICOM caching and archive merging
+
+Depends: dicomscope
+Homepage: http://dicom.offis.de/dscope.php.en
+License: OFFIS
+WNPP: 508990
+Responsible: Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dicomscope/trunk
+Pkg-Description: DICOMscope - DICOM Viewer
+ DICOMscope is a free DICOM viewer which can display uncompressed,
+ monochrome DICOM images from all modalities and which supports
+ monitor calibration according to DICOM part 14 as well as
+ presentation states. DICOMscope offers a print client (DICOM Basic
+ Grayscale Print Management) which also implements the optional
+ Presentation LUT SOP Class. The development of this prototype was
+ commissioned by the "Committee for the Advancement of DICOM" and
+ demonstrated at the European Congress of Radiology ECR 1999. An
+ enhanced version was developed for the "DICOM Display Consistency
+ Demonstration" at RSNA InfoRAD 1999. The current release 3.5.1 has
+ been demonstrated at ECR 2001 and contains numerous extensions,
+ including a print server, support for encrypted DICOM communication,
+ digital signatures and structured reporting.
+ .
+ DICOMscope is not meant as a competition for commercial DICOM
+ viewers. The application is rather a feasibility study for DICOM
+ presentation states. The program is not appropriate to be used in a
+ clinical environment, e.g. for reporting.
+
+Depends: dicom3tools
+Homepage: http://www.dclunie.com/dicom3tools.html
+License: BSD
+WNPP: 508901
+Responsible: Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/dicom3tools/trunk
+Pkg-Description: DICOM medical image files manipulation and conversion tools
+ Command line utilities for creating, modifying, dumping and validating
+ files of DICOM attributes. Support conversion of some proprietary medical
+ image formats to DICOM. Can handle older ACR/NEMA format data, and some
+ proprietary versions of that such as SPI.
+
+Depends: ecg2png
+X-Homepage-old: http://www.cardiothink.com/downloads
+Homepage: http://www.freshports.org/graphics/ecg2png/
+License: GPL
+Pkg-Description: convert scanned electrocardiograms into PNG format
+ This program is designed to convert scanned 12-lead
+ electrocardiograms into PNG format and a web-friendly image size. It
+ assumes that the electrocardiogram (ECG) is printed with a black line
+ on white paper with a red grid.
+ .
+ The problems this program is designed to solve are (1) an ECG scanned
+ at relatively high resolution (300 to 600 dots per inch) imposes a
+ substantial load on the web browser because it contains about 6
+ million pixels which may require 18 to 24 MB of RAM to store for
+ display. Also, (2) typical scanners convert a clean paper ECG into a
+ multitude of colors, include green and blue. The resulting file
+ cannot be compressed efficiently because it does not contain as much
+ redundancy, and thus takes more time to transmit over low-speed
+ network connections.
+Remark: Homepage vanished
+ The homepage of this project that used to be at
+ http://www.cardiothink.com/downloads/ecg2png/ vanished but the source
+ can be downloaded fro instance from
+ http://www.freshports.org/graphics/ecg2png/ .
+
+Depends: kradview
+Homepage: http://www.orcero.org/irbis/kradview/
+License: GPLv3
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kradview/trunk
+Responsible: Andreas Tille <tille at debian.org>
+Pkg-Description: the free DICOM viewer for Linux
+ Kradview is a GPLed viewer of images obtained for some different
+ sources: X-ray, NMR and DICOM-compatible imaging devices that runs on
+ free operating systems. Its aim is a easy to use DICOM viewer with
+ instant rendering of images, no matter the size and the zoom of the
+ DICOM image. It covers the "let's see the the X-ray image" need of
+ the medical professional.
+ .
+ Kradview as been developed in C and C++ using KDE libraries. The
+ parsing, rendering, and processing routines has been developed in C,
+ and the graphical interface has been developed in C++ and includes
+ the former routines with "extern C" for fast use.
+
+Depends: opensourcepacs
+Homepage: http://www.mii.ucla.edu/index.php/MainSite:OpenSourcePacsHome
+License: GPL
+WNPP: 509113
+Responsible: Mathieu Malaterre <mathieu.malaterre at gmail.com>
+Pkg-Description: medical image referral, archiving, routing and viewing system
+ OpenSourcePACS is a free, open source image referral, archiving,
+ routing and viewing system. It adds functionality beyond conventional
+ PACS by integrating wet read functions, implemented through DICOM
+ Presentation State and Structured Reporting standards.
+ .
+ In its first release, OpenSourcePACS delivers a complete wet read
+ system, enabling an imaging clinic or hospital to offer its services
+ over the web to physicians within or outside the institution. In
+ future releases, we hope to incorporate more RIS (dictation,
+ transcription, and reporting) functionality.
+ .
+ OpenSourcePACS is a product of the UCLA Medical Imaging Informatics
+ group (http://www.mii.ucla.edu/).
+
+Depends: pixelmed-dicom-toolkit
+Homepage: http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit
+License: BSD
+Pkg-Description:
+ This is a stand-alone DICOM toolkit that implements code for reading
+ and creating DICOM data, DICOM network and file support, a database
+ of DICOM objects, support for display of directories, images, reports
+ and spectra, and DICOM object validation.
+ .
+ The toolkit is a completely new implementation, which does not depend
+ on any other DICOM tools, commercial or free. It does make use of
+ other freely available pure Java tools for compression and XML and
+ database support.
+
+Suggests: visit
+Homepage: http://www.llnl.gov/visit/
+WNPP: 395573
+License: 3-clause BSD license with additional disclaimers
+Pkg-Description:visualization and graphical analysis tool for viewing scientific data
+ VisIt is a free interactive parallel visualization and graphical
+ analysis tool for viewing scientific data. Users can quickly
+ generate visualizations from their data, animate them through time,
+ manipulate them, and save the resulting images for presentations.
+ VisIt contains a rich set of visualization features so that you can
+ view your data in a variety of ways. It can be used to visualize
+ scalar and vector fields defined on two- and three-dimensional (2D
+ and 3D) structured and unstructured meshes.
+ .
+ VisIt was designed to handle very large data set sizes in the terascale
+ range and yet can also handle small data sets in the kilobyte range.
+
+Depends: mni-autoreg
+Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/
+License: no-free, but GPLed parts
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/contrib/m/mni-autoreg-model/
+Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model
+ This package provides a version of the MNI Average Brain (an average of 305
+ T1-weighted MRI scans, linearly transformed to Talairach space) specially
+ adapted for use with the MNI Linear Registration Package.
+ .
+ * average_305.mnc - a version of the average MRI that covers the whole brain
+ (unlike the original Talairach atlas), sampled with 1mm cubic voxels
+ * average_305_mask.mnc - a mask of the brain in average_305.mnc
+ * average_305_headmask.mnc - another mask, required for nonlinear mode
+Remark: There was some previous work on this software which is stalled currently
+ Michael Hanke agreed to take over his stuff from mentors
+ http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg
+ and
+ http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-autoreg-model
+ to Debian Med svn and start group maintenance.
+
+Depends: mni-n3
+Homepage: http://www.bic.mni.mcgill.ca/software/N3/
+License: BSDish
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://mentors.debian.net/debian/pool/main/m/mni-n3/
+Pkg-Description: MNI Non-parametric Non-uniformity Normalization
+ MNI Non-parametric Non-uniformity Normalization (N3). This package provides
+ the 'nu_correct' tool for unsupervised correction of radio frequency (RF)
+ field inhomogenities in MR volumes. Two packages are provided:
+ * mni-n3 - provides 'nu_correct'
+ * libebtks-dev - MNI support library with numerical types and algorithms
+Remark: There was some previous work on this software which is stalled currently
+ Michael Hanke agreed to take over his stuff from mentors
+ http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=mni-n3
+ to Debian Med svn and start group maintenance.
+
+Depends: brainvisa
+Homepage: http://brainvisa.info/
+License: Free? (CeCill License)
+Pkg-Description: image processing factory for MR images
+ BrainVISA is a software, which embodies an image processing
+ factory. A simple control panel allows the user to trigger some
+ sequences of treatments on series of images. These treatments are
+ performed by calls to command lines provided by different
+ laboratories. These command lines, hence, are the building blocks on
+ which are built the assembly lines of the factory. BrainVISA is
+ distributed with a toolbox of building blocks dedicated to the
+ segmentation of T1-weighted MR images. The product of the main
+ assembly line made up from this toolbox is the following: grey/white
+ classification for Voxel Based Morphometry, Meshes of each hemisphere
+ surface for visualization purpose, Spherical meshes of each
+ hemisphere white matter surface, a graph of the cortical folds, a
+ labeling of the cortical folds according to a nomenclature of the
+ main sulci.
+
+Depends: maris
+Homepage: http://maris.homelinux.org/
+License: GPL
+Pkg-Description: package suite for Radiological Workflow
+ The MARiS Project goal is to realize a package suite for Radiological
+ Workflow using Open Source tools and technologies in according with
+ IHE guidelines. The architecture of the single packages is based on
+ the concept of IHE actor: this is very useful to develope a system
+ that is an ensamble of single pieces that cooperate together using
+ IHE profiles.
+
+Depends: via
+Homepage: http://www.cbs.mpg.de/institute/software/lipsia
+License: GPL
+WNPP: 521328
+Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/via.git
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/via-bin
+Pkg-Description: library and tools for volumetric image analysis
+ This package provides a toolkit for functional and structural (medical)
+ image data processing. It consists of a library of about 50 different
+ programs ranging from simple data handling routines and viewers to
+ complex image transformation algorithms.
+ .
+ All tools operate on data in VISTA format. The package contains several
+ converters from e.g. PNG, PGM or PNM to this data format and back.
+
+Depends: lipsia
+Homepage: http://www.cbs.mpg.de/institute/software/lipsia
+License: GPL
+WNPP: 521412
+Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/lipsia.git
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/lipsia
+Pkg-Description: analysis suite for MRI and fMRI data
+ Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)
+ .
+ This is a software package for the data processing and evaluation of
+ functional magnetic resonance images. The analysis of fMRI data comprises
+ various aspects including filtering, spatial transformation, statistical
+ evaluation as well as segmentation and visualization. All these aspects are
+ covered by LIPSIA. For the statistical evaluation, a number of well established
+ and peer-reviewed algorithms were implemented in LIPSIA that allow an effcient
+ and user-friendly processing of fMRI data sets. As the amount of data that must
+ be handled is enormous, an important aspect in the development LIPSIA was the
+ efficiency of the software implementation.
+ .
+ LIPSIA operates exclusively on data in the VISTA data format. However, the
+ package contains converters for medical image data in iBruker, ANALYZE and
+ NIfTI format -- converting VISTA images into NIfTI files is also supported.
+
+Depends: micromanager
+Homepage: http://www.micro-manager.org/
+License: free, but some nonfree parts with NDA
+Responsible: Johan Henriksson <johan.henriksson at ki.se>
+Pkg-URL: http://mahogny.areta.org/temp/debs/
+Pkg-Description: imaging and control of automated microscopes, shutters, cameras etc.
+ µManager is an Open Source software package for imaging and control
+ of automated microscopes. Together with ImageJ, a popular image processing
+ package, μManager provides a comprehensive imaging solution – comparable to
+ commercially available ones.
+ .
+ Unfortunately there is a pile of dirty licenses involved so I'm not sure
+ this is ready for Debian yet. Some of the code cannot be given out and
+ some drivers require kernel modules to be built. You have to sign NDAs
+ to get access to all the code.
+
+Suggests: mrisim
+Homepage: http://packages.bic.mni.mcgill.ca/tgz/
+License: BSD-like
+Pkg-Description: simulator for magnetic resonance imaging data
+ mrisim is a simple Magnetic Resonance Imaging (MRI) simulation program
+ which produces MINC volumes from a segmented and labelled brain phantom.
+ It allows intrinsic tissue parameters (T1, T2...) and pulse sequence
+ parameters (TR, TE ...) to be specified and then produces simulated
+ images with noise. Currently, no artifacts are implemented.
+
+
+Depends: odin
+Homepage: http://od1n.sourceforge.net/
+License: GPL
+WNPP: 410318
+Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/odin.git
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/odin
+Pkg-Description: develop, simulate and run magnetic resonance sequences
+ C++ software framework to develop, simulate and run magnetic resonance
+ sequences on different platforms. It is
+ .
+ - State-of-the-Art: Contemporary magnetic resonance imaging techniques
+ are available, for example sequence modules for echo-planar imaging
+ and spiral-imaging, parallel imaging with GRAPPA reconstruction,
+ two-dimensional pulses and field-map-based distortion corrections.
+ .
+ - Easy-to-Use: All common steps, from compiling your sequence to
+ plotting or simulating it, can be performed within a graphical user
+ interface.
+ .
+ - Hardware Independent: ODIN runs on a variety of operating systems and
+ scanners. Once you develop a sequence, it can be executed/simulated
+ on very different hardware, ranging from a real-time sequence
+ controller to your personal workstation.
+ .
+ - Truly Object-Oriented: Written in C++ with an object-oriented design,
+ ODIN is very modular, flexible and requires very little code to
+ write: The sequences that come with ODIN are easy to understand and
+ modify.
+
+Depends: fiji
+Homepage: http://pacific.mpi-cbg.de/
+Responsible: Mark Longair <mark-debianlists at longair.net>
+Pkg-URL: http://pacific.mpi-cbg.de/wiki/index.php/Downloads
+Pkg-Description: The Fiji image processing suite (based on ImageJ)
+ Fiji is a project aiming at simplifying:
+ * the installation of ImageJ
+ * the usage of ImageJ
+ * the usage of specific, powerful ImageJ plugins
+ * the development of plugins using ImageJ
+Remark: About packaging status the authors said:
+ See the thread on the Debian Med mailing list at:
+ http://lists.debian.org/debian-med/2009/04/msg00059.html
+ - We've been working to get rid of, or replace, any remaining
+ non-DFSG licensed plugins, but there's at least one left.
+ The bug for tracking this is here:
+ http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19
+ - At the moment Fiji depends on sun-java6 rather than openjdk.
+ - The packages are rather large at the moment (about 35MiB).
+ This is mostly due to bundling various components with Fiji
+ that could be satisfied as dependencies in Debian, such as
+ junit, jruby, etc. but I haven't had time to work on
+ separating those out.
+ - Fiji uses a modified version of ImageJA (which again is
+ bundled into the fiji package) rather than depending on the
+ imagej Debian package created by people on this list.
+ - One of the aims of Fiji was to make Benjamin Schmid's
+ Java3D-based 3D viewer plugin work out-of-the-box, since
+ people often had trouble installing it manually. At the time
+ when I first made these packages there were no java3d
+ packages in Debian, but now that these are in sid we should
+ eventually be able to switch to using those.
Added: projects/med/tags/1.3/tasks/imaging-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/imaging-dev?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/imaging-dev (added)
+++ projects/med/tags/1.3/tasks/imaging-dev Sat Jun 23 12:46:46 2012
@@ -1,0 +1,110 @@
+Task: Imaging Development
+Description: Debian Med packages for medical image development
+ This metapackage will install Debian packages which might be useful
+ for developing applications for medical image processing.
+
+Depends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev
+
+Depends: libnifti1-dev
+
+Depends: libigstk3-dev
+
+Suggests: igstk-examples
+
+Depends: libinsighttoolkit3-dev
+
+Suggests: insighttoolkit3-examples
+
+Suggests: libnifti-doc
+
+Suggests: libvtk5
+
+Depends: libvolpack1-dev
+
+Depends: libgdcm2-dev
+
+Suggests: python-libavg
+Why: Homepage (http://www.libavg.de) shows some potential medical applications
+
+Depends: python-mvpa
+Why: Suggested by maintainer Michael Hanke <michael.hanke at gmail.com>
+
+Depends: python-nipy
+
+Depends: odin
+Homepage: http://od1n.sourceforge.net/
+License: GPL
+WNPP: 410318
+Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/odin.git
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/html/pkgs/odin
+Pkg-Description: Object Oriented Development Interface for NMR
+ C++ software framework to develop, simulate and run magnetic resonance
+ sequences on different platforms. It is
+ .
+ State-of-the-Art: Contemporary magnetic resonance imaging techniques
+ are available, for example sequence modules for echo-planar imaging
+ and spiral-imaging, parallel imaging with GRAPPA reconstruction,
+ two-dimensional pulses and field-map-based distortion corrections.
+ .
+ Easy-to-Use: All common steps, from compiling your sequence to
+ plotting or simulating it, can be performed within a graphical user
+ interface.
+ .
+ Hardware Independent: ODIN runs on a variety of operating systems and
+ scanners. Once you develop a sequence, it can be executed/simulated
+ on very different hardware, ranging from a real-time sequence
+ controller to your personal workstation.
+ .
+ Truly Object-Oriented: Written in C++ with an object-oriented design,
+ ODIN is very modular, flexible and requires very little code to
+ write: The sequences that come with ODIN are easy to understand and
+ modify.
+
+Depends: libvista2-dev
+Homepage: http://mia.sourceforge.net/
+License: GPL
+Pkg-Description: software environment for computer vision research
+ Vista is a software environment for computer vision research. It is
+ designed to support not only images, but also edge sets, camera models,
+ and more complex data structures. Vista includes libraries of common
+ computer vision and image processing algorithms. It is written in
+ ANSI C, for UNIX platforms running X Windows, and it is freely available.
+ The original development was done at University of British Columbia
+ (http://www.cs.ubc.ca/nest/lci/vista/vista.html).
+ .
+ Because the development was stalled by the original authors the
+ development continued in the "Tools for Medical Image Analysis"
+ framework (http://mia.sourceforge.net/) which is maintained by
+ Max Planck Institute of Cognitive Neuroscience
+ (http://www.cns.mpg.de/).
+ .
+ This is the development package.
+
+Depends: libmni-perllib-perl
+Homepage: http://packages.bic.mni.mcgill.ca/tgz/
+License: Artistic License
+Responsible: Michael Hanke <michael.hanke at gmail.com>
+Pkg-URL: http://apsy.gse.uni-magdeburg.de/svn/fsl/libmni-perllib-perl/trunk/debian/
+Pkg-Description: The MNI Perl Library
+ Collection of various Perl module used by other MNI software
+ packages.
+Remark: There was some previous work on this software which is stalled currently
+ Michael Hanke agreed to take over his stuff from mentors
+ http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=libmni-perllib-perl
+ to Debian Med svn and start group maintenance.
+
+Depends: rumba
+Homepage: http://www.rumba.rutgers.edu/soft/
+License: Artistic
+Pkg-URL: http://itanix.rutgers.edu/rumba/dists/unstable/perspect/source/science/
+Pkg-Description: analysis of MRI anatomical and functional datasets
+ RUMBA (Rutgers University Mind Brain Analysis) toolkit was developed for the
+ analysis of MRI anatomical and functional datasets. The toolkit provides means
+ to perform I/O, registration, motion correction, filtering, PCA, ICA, GLM, and
+ visualization. To take advantage of speedy C++ written I/O and processing
+ routines, bindings to high level programming (python) or computational (R)
+ environments are available.
+Remark: Work done outside Debian
+ There seems to be a lot of packaging stuff just done by upstream
+ guessed from http://itanix.rutgers.edu/rumba/ and the project homepage.
Added: projects/med/tags/1.3/tasks/laboratory
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/laboratory?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/laboratory (added)
+++ projects/med/tags/1.3/tasks/laboratory Sat Jun 23 12:46:46 2012
@@ -1,0 +1,22 @@
+Task: Laboratory
+Description: Debian Med suggestions for medical laboratories
+ Currently Debian Med does not yet contain any software which is
+ specifically intended to run a medical laboratory. We just provide a
+ list of Free Software that might be used and which might be included
+ into Debian at a later point in time provided somebody is willing to
+ take over the packaging work.
+
+Depends: openelis
+Homepage: http://openelis.uhl.uiowa.edu/
+License: UIRF Open-source Based Public Software License
+Pkg-Description: Enterprise Laboratory Information System
+ OpenELIS is a robust Enterprise Laboratory Information System built around an
+ extensible and scalable framework. OpenELIS is designed and developed through
+ the collaborative efforts of Public Health Laboratories to accommodate
+ business processes that are common to all public health laboratories;
+ encompassing clinical, environmental, newborn screening, and animal testing.
+ .
+ The goal of the OpenELIS team is to develop a state of the art system that
+ is economically sustainable by reducing both initial investment and ongoing
+ maintenance costs. By using an open source approach, we ensure that the project
+ will continue to evolve and meet the changing needs of the community.
Added: projects/med/tags/1.3/tasks/pharmacy
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/pharmacy?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/pharmacy (added)
+++ projects/med/tags/1.3/tasks/pharmacy Sat Jun 23 12:46:46 2012
@@ -1,0 +1,7 @@
+Task: Pharmacy
+Description: Debian Med packages for pharmaceutical research
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Depends: chemtool
Added: projects/med/tags/1.3/tasks/physics
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/physics?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/physics (added)
+++ projects/med/tags/1.3/tasks/physics Sat Jun 23 12:46:46 2012
@@ -1,0 +1,79 @@
+Task: Physics
+Description: Debian Med packages for medical physicists
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
+Depends: paw++
+Why: Just depend from the user friendly version because it is easier to
+ povide a menu item
+
+Depends: paw
+Why: This is for the purists with exactly the same functionality as paw++
+
+Suggests: paw-demos
+
+Depends: octave3.0
+
+Depends: r-base | r-base-core
+Why: "r-base" is a metapackage and it is better to have a default
+ alternative -- Dirk Eddelbuettel <edd at debian.org>
+
+Depends: biosig
+Homepage: http://biosig.sf.net
+License: GPL
+Pkg-Description: library for biomedical signal processing
+ BioSig is an open source software library for biomedical signal
+ processing, featuring for example the analysis of biosignals such as
+ the electroencephalogram (EEG), electrocorticogram (ECoG),
+ electrocardiogram (ECG), electrooculogram (EOG), electromyogram
+ (EMG), respiration, and so on. Major application areas are:
+ Neuroinformatics, brain-computer interfaces, neurophysiology,
+ psychology, cardiovascular systems and sleep research. The aim of the
+ BioSig project is to foster research in biomedical signal processing
+ by providing open source software tools for many different
+ applications. Generally, many concerns have to be addressed in this
+ scientific field. BioSig handles this by providing solutions for data
+ acquisition, artifact processing, quality control, feature
+ extraction, classification, modeling, data visualization, and so on.
+ .
+ BioSig consists of some (more or less) coherent parts, for more
+ details take a look at the project page:
+ * BioSig for Octave and Matlab (biosig4octmat): A toolbox for Octave
+ and Matlab with powerful data import and export filters, feature
+ extraction algorithms, classification methods, and a powerful
+ viewing and scoring software.
+ * BioSig for C/C++ (biosig4c++) containing:
+ reading and writing routines for different biosignal data formats.
+ - libbiosig - a library for reading and writing of a number of data
+ formats. libbiosig is used by save2gdf, mexSLOAD and SigViewer
+ - save2gdf - a converter between different data formats, and can be used
+ to show the header information
+ - mexSLOAD is a MEX-interface for loading biosignal data into Octave
+ (its much faster than the pure M-tools from biosig4octmat). It requires
+ Octave-headers and libbiosig
+ * SigViewer (sigviewer): A stand-alone viewing and scoring software for
+ biosignals (especially for EEG signals) based on C++ and the
+ platform-independent GUI toolkit Qt 4.
+ * rtsBCI (rtsbci): A real-time BCI system implemented in Matlab and
+ Simulink.
+ * BioProFeed (bioprofeed)
+ * BCIx (bcix)
+
+Depends: gate
+Homepage: http://www.opengatecollaboration.org
+License: LGPL
+WNPP: 431425
+Responsible: Nicolas Spalinger <nicolas.spalinger at healthgrid.org>
+Pkg-Description: Geant4 Application for Emission Tomography
+ GATE incorporates the Geant4 libraries in a modular, versatile, and
+ scripted simulation toolkit which is adapted to the field of nuclear
+ medicine both in PET (Positron Emission Tomography) and SPECT (Single
+ Photon Emission Computer Tomography). It allows the accurate description
+ of time-dependent phenomena such as source or detector movement and
+ source decay kinetics. The ability to synchronize all time-dependent
+ components allows a coherent description of the acquisition process. It
+ makes it possible to perform realistic simulations of data acquisitions
+ in time.
+
Added: projects/med/tags/1.3/tasks/practice
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/practice?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/practice (added)
+++ projects/med/tags/1.3/tasks/practice Sat Jun 23 12:46:46 2012
@@ -1,0 +1,260 @@
+Task: Practice
+Description: Debian Med packages for practice management
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for practitioners to manage their practice.
+
+Depends: gnumed-client
+
+Depends: gnumed-server
+
+Depends: libchipcard-tools
+Why: Reading German "Gesundheitskarte"
+
+Depends: aeskulap
+
+Depends: medintux
+Homepage: http://medintux.org/medintux/en/
+License: CeCILL (free)
+Pkg-Description: Medical practice management system
+ MedinTux is a powerful medical software, multiuser (using MySQL for data storage),
+ easy-to-use, complete, working from the GP to the hospital.
+ .
+ Help wanted: Unfortunately, MedinTux is written in french, closing its use to many
+ countries in the world. Help is wanted to translate
+ .
+ * The GUI (directly in the source code, which will be reverse translated later
+ to french, using Qt Linguist)
+ * The documentation and installation instructions
+ .
+ Any person with real french to english skill is wellcome.
+ Please, contact Gérard Delafond : gerard-at-delafond.org
+
+Depends: mirth
+Homepage: http://www.mirthproject.org/
+License: MPL 1.1
+Pkg-Description: HL7 integration engine
+ "Swiss army knife" HL7 integration engine. Specifically designed for
+ HL7 message integration, Mirth provides the necessary tools for developing,
+ deploying, and monitoring interfaces.
+ .
+ Filtering can be performed on incoming messages using the default message
+ filters that are included with Mirth, or your own custom filtering scripts.
+ Mirth's web interface makes it easy to write new scripts by proving a
+ template and editing field that allows you to validate your script code.
+ Mirth also supports filters written in Java if you require more complex
+ filtering options.
+
+Depends: tinyheb
+Homepage: http://tinyheb.sourceforge.net/
+License: GPL
+Pkg-URL: http://home.arcor.de/thomas.baum/tinyheb/source/
+Pkg-Description: billing system for midwives
+ This billing system enables midwives to exchange data with health
+ insurances in Germany (compliant to §302 SGB V).
+
+Ignore: clearhealth
+Homepage: http://www.clear-health.com/
+License: GPL
+Pkg-Description: medical practice management
+ For larger practices or those with multiple locations ClearHealth
+ Advantage is an enterprise scalable system to meet the most demanding
+ needs.
+ .
+ The ClearHealth medical suite now offers a next generation set of
+ capabilities to practices large and small. Combining best of breed
+ scheduling, patient management, EMR, reporting, document storage,
+ labs, prescriptions and billing it gives you the tools you need to
+ effectively run your practice and keep your focus where it counts, on
+ improving patient care.
+ .
+ With support for a huge variety of payers and clearing houses you
+ have many options in who you can bill electroncally. Paper forms
+ support for the HCFA (CMS 1500) format as well as UB92 support.
+ Scheduling
+ .
+ Practice management begins with scheduling, while not specifically a
+ medical problem as any doctor knows there are several unique aspects
+ of medical scheduling that can make life miserable for the front end
+ staff. ClearHealth scheduling was built from the ground up in close
+ consultation with medical professionals to ensure that it meets those
+ special needs. Being extremely flexible you can schedule based on
+ providers, rooms, or equipment across facilities and regions.
+Comment: I do not really remember why this is set to "Ignore" - my
+ only guess is that it once was GPL and now the homepage quoted above
+ seems to provide some proprietary software. Some investigation might
+ be needed (at).
+ .
+ The guessing above is manifested by the fact that the source code
+ repository of clearhealth which was linked from http://www.op-en.org/
+ vanished.
+
+Depends: mirrormed
+Homepage: http://www.mirrormed.org/
+License: GPL
+Pkg-Description: EHR and practice management system
+ MirrorMed is a free and open source EHR and practice management
+ system written in PHP. MirrorMed is a web-based application that is
+ capable of running a healthcare practice. MirrorMed shares code with
+ FreeMED, and OpenEMR. MirrorMed is primarily sponsored by SynSeer.
+
+Depends: elexis
+Homepage: http://sourceforge.net/projects/elexis
+License: Eclipse Public License
+Pkg-Description: medical practice managemant system for use in Switzerland
+ An Eclipse RCP program for all aspects of a medical practice:
+ electronic medical record (EMR), laboratory findings etc., as well as
+ accounting, billing (swiss TARMED-System, other systems to be
+ developped) and other daily work.
+
+Depends: freeb
+Homepage: http://freeb.org/
+License: GPL
+Pkg-Description: Medical Bill formating module
+ FreeB is Medical Bill formating module. It is designed to be used with any
+ EHR system that tracks basic demographics, procedure codes and diagnosis
+ codes. An EHR sends the basic billing data to FreeB using a simple XML-based
+ interface (XML-RPC or SOAP as needed). FreeB then handles the bill formating
+ and bill revision. FreeB has standard templates for X12 837, HFCA 1500 (now
+ the NPI modified CMS-1500) and UB-92 series formats. FreeB is designed so that
+ it can send bills to a printer, to a payers web interface, or to a
+ clearinghouse. FreeB also performs bill revision, as you modify the claim
+ data in order to meet the payor requirements, FreeB keeps track of those
+ changes over time so that you can easily see the progression of the claim
+ over time. The current version of FreeB is written in PHP and uses the Smarty
+ template language for bill templates. FreeB has a web interface that allows
+ users to modify any aspect of a claim, and send groups of claims in different
+ directions.
+ .
+ FreeB 1.0 (Perl) is still used by the OpenEMR project. FreeB 1.0 was rewritten
+ as REMITT which used by the FreeMED project.
+
+Depends: freemed
+Homepage: http://www.freemedsoftware.org/
+License: GPL
+Pkg-URL: http://downloads.sourceforge.net/freemed/freemed_0.8.4-1_all.deb?use_mirror=mesh
+Pkg-Description: Electronic Medical Record and Practice Management system
+ Electronic Medical Record and Practice Management system for medical providers
+ that runs in any web browser in multiple languages. It provides an XML-RPC
+ backend and multiple import and export formats, as well as reporting and other
+ features.
+
+Depends: elementalclinic
+Homepage: http://www.elementalclinic.com/
+License: GPL2+
+Responsible: Hans Dieter Pearcey <hdp at opensourcery.com>
+Pkg-URL: http://svn.opensourcery.com/public/ubuntu/pool/main/e/elementalclinic/
+Pkg-Description: Electronical Medical Health record system for mental health
+ Elemental Clinic is medical records management system for mental health
+ professionals.
+ .
+ * Implement an affordable web-based alternative to paper records keeping
+ * Train and support clinicians to get the most from your EMR
+ * Customize software to fit unique practice needs
+
+Depends: openemr
+Homepage: http://www.oemr.org/
+License: GPL
+Pkg-Description: medical practice management
+ OpenEMR is a free medical practice management, electronic medical records, prescription
+ writing, and medical billing application. These programs are also referred to as
+ electronic health records. It is a free open source replacement for medical applications
+ such as Medical Manager, Health Pro, and Misys. It features support for EDI billing to
+ clearing houses such as MedAvant and ZirMED using ANSI X12. Medical claim and accounts
+ receivable are accomplished through SQL-Ledger, which has been customized. Calendar
+ features include categories for appointment types, colors associated with appointment
+ types, repeating appointments, and the ability to restrict appointments based on type.
+ There are customizable medical encounter forms, support for voice recognition software,
+ and electronic or scanned digital document management for records.
+ .
+ The community is dedicated to guarding OpenEMR's status as a free, open source software
+ solution for medical practices. Its members are comprised of software developers, as well
+ as physicians and those with extensive medical and billing knowledge, all with the common
+ goal of making OpenEMR a viable alternative to its proprietary counterparts.
+ .
+ The OpenEMR community strives to work together to create a high-quality electronic medical
+ record and practice management system. Through open collaboration, the community is molding
+ a stable, yet continuously improving product, thanks to the efforts of developers across
+ the globe, brought together by their tenacity and the connectivity of the Internet.
+
+Depends: clearhealth
+Homepage: http://www.op-en.org/site/clearhealth
+License: GPL
+Pkg-Description: Medical practice management system
+ ClearHealth is a Ppractice Management System to address the big five features: Medical
+ Billing, Medical Accounts Recievable, Scheduling, Access Control, and EMR.
+
+Suggests: openpms
+Homepage: http://sourceforge.net/projects/openpms
+License: GPL
+Pkg-Description: medical billing, scheduling, and account management system
+ HIPAA compliant medical billing, scheduling, and account management system. Integrated
+ with x12 standard electronic transactions, OpenBilling XML standards, and hcfa-1500
+ legacy support. Complete cross platform performance with java 2 standards.
+Remark: Status of this software
+ This project has not issued any release since March 2004 and
+ thus might be considered dead. There are some chances to cherry pick some code from
+ SourceForge repository.
+
+Suggests: resmedicinae
+Homepage: http://resmedicinae.sourceforge.net/
+License: GPL:
+Pkg-Description: comprising software solution for use in medicine
+ Res Medicinae is to become a comprising software solution for use in Medicine which combines
+ intuitive ease of use with great flexibility, reached through the usage of CYBOP technology.
+ It wants to adhere to common standards for medical software, wherever useful, and will thus
+ be open to other systems. Using the CYBOL language, users are enabled to, themselves, modify
+ applications.
+ .
+ Res Medicinae is the attempt to overcome high pricing in the realm of Medical Information
+ Systems and to provide users with a free, stable, secure, platform-independent, extensive
+ system.
+ .
+ This project does not provide a complete solution for medical practice. It will take another
+ couple of years before being so far.
+
+Suggests: sqlclinic
+Homepage: http://www.sqlclinic.net/
+License: GPL
+Pkg-Description: intranet solution for Saint Vincents Catholic Medical Centers of New York
+ This is a complete clinical and administrative application for providers of psychiatric
+ housing, although the software is designed to accommodate an entire Community Mental Health
+ Care Center (CMHC) or private practitioners (both clinical social workers and psychiatrists)
+ working in behavioral health. Technical support is free via mailing lists. Support contracts
+ are available from Saint Vincent Catholic Medical Centers of New York.
+ .
+ Features:
+ * Administrative Tools
+ * Built In DBA Utilities
+ * Complete Clinical Chart
+ * Email Alerts, Reports and Reminders
+ * Intake and Placement Tracking
+ * Integrated DSM IV
+ * Quality Assurance Instruments
+ * Purchase Orders
+ * Unit (Shift) Logs
+ * Work Orders
+
+X-Comment: torch seems to be dead (last release in 2004)
+ Sourceforge page: http://sourceforge.net/projects/op-torch/
+
+X-Comment: Circare project seems to be dead
+
+X-Comment: OIO project seems to be dead
+ Homepage: http://www.txoutcome.org/
+
+X-Comment: Open PM ToolWorks seems to be dead
+
+Suggests: openrep
+Homepage: http://www.homeopathyonline.org/about_OpenRep.html
+License: GPLv3 or later
+WNPP: 533044
+Responsible: Y Giridhar Appaji Nag <appaji at debian.org>
+Pkg-Description: software for homeopathic repertorization and viewing materia medicae
+ OpenRep is a Java desktop application designed to serve as a homeopathic
+ software with capabilities to open and use multiple repertories, perform
+ repertorizations and view its results, manage patients and view different
+ materia medicae. It is also designed to save and load data in human readable
+ xml format.
+Remark: scientific use?
+ Please read the thread about homeopathic software on the Debian Med mailing
+ list starting at http://lists.debian.org/debian-med/2009/06/msg00028.html .
Added: projects/med/tags/1.3/tasks/psychology
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/psychology?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/psychology (added)
+++ projects/med/tags/1.3/tasks/psychology Sat Jun 23 12:46:46 2012
@@ -1,0 +1,22 @@
+Task: Psychology
+Description: Debian Med packages for psychology
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for psychological research.
+
+Depends: python-pyepl
+
+Depends: praat
+
+Depends: r-cran-foreign, r-cran-psy, psignifit
+Why: analysis packages of particular relevance for psych. data
+
+Depends: psychopy
+
+Depends: visionegg
+Homepage: http://www.visionegg.org
+License: LGPL
+WNPP: 365856
+Pkg-Description: Python library for 2D/3D visual stimulus generation
+ The Vision Egg is a programming library that uses standard, inexpensive
+ computer graphics cards to produce visual stimuli for vision research
+ experiments.
Added: projects/med/tags/1.3/tasks/statistics
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/statistics?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/statistics (added)
+++ projects/med/tags/1.3/tasks/statistics Sat Jun 23 12:46:46 2012
@@ -1,0 +1,12 @@
+Task: Statistics
+Description: Debian Med statistics
+ This metapackage will install packages which are helpful to do statistics
+ with a special focus on tasks in medical care.
+
+Depends: r-cran-qvalue
+
+Depends: r-cran-randomforest
+
+Suggests: science-statistics
+Why: This more or less includes all statistics relevant packages which might be
+ a bit to much for medical purposes - so it is only suggested.
Added: projects/med/tags/1.3/tasks/tools
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/tools?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/tools (added)
+++ projects/med/tags/1.3/tasks/tools Sat Jun 23 12:46:46 2012
@@ -1,0 +1,36 @@
+Task: Tools
+Description: Debian Med several tools
+ This metapackage will install tools for several purposes in health care.
+ Currently it contains some simple programs for Personal Health.
+
+Depends: mencal, cycle, pondus
+
+Suggests: cl-pubmed
+Why: Strong dependency would cost installing a large amount of Common Lisp tools which in most cases is not worth the effort
+
+Depends: mssstest
+
+Depends: wgerman-medical, hunspell-de-med
+
+Depends: quitcount
+
+Depends: linuxorg-pcal
+Homepage: http://linuxorg.sourceforge.net/about_m.phtml#pcal
+License: GPL
+Pkg-Description: assist in women menstrual cycles tracking and fertility periods prediction
+ Periodic Calendar is a GUI utility which assists in women menstrual
+ cycles tracking and fertility periods prediction. This information
+ can be used either to became pregnant or to prevent pregnancy. The
+ fertility prediction is based on the calendar method which is not
+ very precise. It is not recommended to use this method alone for the
+ birth control.
+
+Depends: hunspell-en-med
+Homepage: http://e-medtools.com/openmedspel.html
+License: GPL
+Pkg-Description: English medical spelling word list
+ OpenMedSpel includes nearly 50,000 medical terms ranging from abdominis
+ to zygomatic, which allows you to concentrate on your work instead of
+ looking up words in a medical dictionary that are not in a standard USA
+ English spelling dictionary.
+
Added: projects/med/tags/1.3/tasks/typesetting
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.3/tasks/typesetting?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.3/tasks/typesetting (added)
+++ projects/med/tags/1.3/tasks/typesetting Sat Jun 23 12:46:46 2012
@@ -1,0 +1,11 @@
+Task: Typesetting
+Description: Debian Med support for typesetting and publishing
+ This metapackage will install Debian packages that might be helpful
+ for typesetting and publishing in medical care and structural
+ biology.
+
+Depends: texlive-science, texlive-latex-extra
+
+Suggests: kbibtex
+
+Suggests: bibus
Added: projects/med/tags/1.4/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.4/debian/control?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.4/debian/control (added)
+++ projects/med/tags/1.4/debian/control Sat Jun 23 12:46:46 2012
@@ -1,0 +1,192 @@
+# This file is autogenerated via make -f debian/rules dist. Do not edit!
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends-Indep: blends-dev (>= 0.6.8)
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
+
+Package: med-tasks
+Architecture: all
+Depends: tasksel
+Description: Debian Med tasks for tasksel
+ This package provides Debian Med tasks in tasksel.
+ .
+ These tasks are described in detail at
+ http://debian-med.alioth.debian.org/tasks/
+
+Package: med-config
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.8)
+Conflicts: med-common
+Replaces: med-common
+Provides: med-common
+Description: Debian Med Project config package
+ This package provides the basic infrastructure of all med-* packages and is
+ needed by them.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med using debconf.
+ .
+ Other packages in Debian Med Project are:
+ .
+ * med-bio for biological research
+ * med-bio-dev for developing applications in biological research
+ * med-cms for publicating a medical site on the internet
+ * med-epi for epidemiology
+ * med-imaging for image processing
+ * med-imaging-dev for developing applications for image processing
+ * med-pharmacy for pharmaceutical research
+ * med-physics for radiation oncology, diagnostic imaging, related fields
+ * med-practice for general practitioners
+ * med-tools contains miscellaneous tools
+ * med-typesetting depends from useful tools for typesetting
+ .
+ Note: All these packages are so called metapackages. This means they are not
+ executable programs, but only links to other packages. This way you will
+ conveniently get all the non-commercial medical software which is available
+ for Debian GNU/Linux.
+
+
+Package: med-bio
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: adun.app, alien-hunter, altree, amap-align, autodock, ballview, blast2, boxshade, bwa, dialign, dialign-tx, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, gamgi, garlic, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, kalign, last-align, loki, mafft, maq, massxpert, melting, mipe, mummer, muscle, mustang, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, perlprimer, phyml, plasmidomics, poa, primer3, probcons, proda, pymol, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, readseq, rnahybrid, samtools, seaview, sibsim4, sigma-align, sim4, ssake, staden-io-lib-utils, t-coffee, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
+Suggests: acedb-other, acedb-other-belvu, acedb-other-dotter, act, agdbnet, amos-assembler, amoscmp, arb, artemis, asap, autodocktools, axparafit, axpcoords, bambus, beast-mcmc, big-blast, bio-mauve, blixem, bowtie, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, clustalw, clustalw-mpi, clustalx, cluster3, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cytoscape, das-proserver, dazzle, decipher, dotter, dotur, ecell, elph, embassy-phylip, emboss-explorer, emboss-kaptain, est-db, estferret, estscan, exalt, excavator, fasta, fastx-toolkit, figaro, finex, fluctuate, forester, galaxy, gbioseq, gbrowse, genesplicer, genetrack, genezilla, genographer, glimmerhmm, gmv, grogui, haploview, hawkeye, hexamer, jalview, jigsaw, jmol, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, martj, mauvealigner, maxd, melting-gui, meme, mesquite, migrate, minimus, mira, mirbase, molekel, molphy, mozilla-biofox, mrbayes, msatfinder, mummergpu, murasaki, mview, ncoils, ngila, obo-edit, oligoarrayaux, omegamap, operondb, paml, partigene, patman, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, plink, populations, prank, proalign, profit, prot4est, pyrophosphate-tools, qtlcart, r-ape, r-other-genabel, raster3d, raxml, rbs-finder, recombine, repeatfinder, reputer, roche454ace2caf, rose, rosetta, seq-gen, seqan-apps, sequenceconverter.app, smile, spice, splitstree, ssaha, tacg, taverna, taxinspector, tetra, tigr-assembler, tm-align, trace2dbest, tracetuner, transtermhp, treebuilder3d, treeplot, treevolve, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+
+Package: med-bio-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libqsearch-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats, seqan-dev
+Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbio-mage-utils-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, r-cran-rocr
+Description: Debian Med packages for development of micro-biology applications
+ This metapackage will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
+Package: med-cms
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Suggests: zope-zms
+Description: Debian Med content management systems
+ This metapackage will install packages which are useful to build a
+ content management system for medical care.
+
+Package: med-epi
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: epigrass, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epitools
+Suggests: netepi-analysis, netepi-collection, r-cran-diagnosismed, r-cran-epir, r-cran-msm, r-cran-surveillance
+Description: Debian Med epidemiology related packages
+ This metapackage will install tools that are useful in epidemiological
+ research. Several packages making use of the GNU R data language for
+ statistical investigation. It might be a good idea to read the paper
+ "A short introduction to R for Epidemiology" at
+ http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
+
+Package: med-imaging
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, amide, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, fslview, gwyddion, imagej, libgdcm-tools, lipsia, medcon, minc-tools, nifti-bin, odin, python-mvpa, python-nifti, python-nipy, slicer, sofa-apps, via-bin, xmedcon
+Suggests: afni, bioimagesuite, blox, brainvisa, caret, cdmedicpacs, conquest-dicom-server, dcm4che, devide, dicom4j, dicomscope, drjekyll, ecg2png, fiji, fsl, imagemagick, imview, kradview, libvista2, maris, mesa-test-tools, micromanager, mni-autoreg, mni-n3, mrisim, opendicom.net, openelectrophy, opensourcepacs, piano, pixelmed, pixelmed-dicom-toolkit, pngquant, python-nipype, stir, visit
+Description: Debian Med imaging packages
+ This metapackage will install Debian packages which might be useful in
+ medical image processing.
+ .
+ It installs several packages supporting DICOM (Digital Imaging and
+ Communications in Medicine) which is the de-facto standard for medical
+ image management. The standard defines data structures and services for
+ the exchange of medical images and related information. The latest release
+ has been published in 2008 and consists of 18 parts.
+ .
+ For more information, you can visit the NEMA homepage
+ http://medical.nema.org/ .
+ .
+ The status of the official DICOM base standard plus all the
+ supplements and correction items are summarized at David Clunie's webpage:
+ http://www.dclunie.com/dicom-status/status.html
+ where you'll find direct links to the most recent yearly edition
+ ftp://medical.nema.org/medical/dicom/2008/ .
+
+Package: med-imaging-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cimg-dev, ctn-dev, libcv-dev, libgdcm2-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti1-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-mvpa, python-nipy
+Suggests: gmic, igstk-examples, insighttoolkit3-examples, libigstk3-dev, libmni-perllib-perl, libnifti-doc, libvista2-dev, libvtk5, python-libavg, python-nipype, rumba
+Description: Debian Med packages for medical image development
+ This metapackage will install Debian packages which might be useful
+ for developing applications for medical image processing.
+
+Package: med-pharmacy
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: chemtool
+Description: Debian Med packages for pharmaceutical research
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Package: med-physics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: octave3.2, paw, paw++, r-base | r-base-core
+Suggests: biosig, gate, paw-demos
+Description: Debian Med packages for medical physicists
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
+Package: med-practice
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, gnumed-client, gnumed-server, libchipcard-tools
+Suggests: clearhealth, edfbrowser, elementalclinic, elexis, freeb, freemed, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, resmedicinae, sqlclinic, tinyheb
+Description: Debian Med packages for practice management
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for practitioners to manage their practice.
+
+Package: med-psychology
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: praat, psignifit, psychopy, python-pyepl, r-cran-foreign, r-cran-psy
+Suggests: visionegg
+Description: Debian Med packages for psychology
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for psychological research.
+
+Package: med-statistics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: r-cran-qvalue, r-cran-randomforest
+Suggests: science-statistics
+Description: Debian Med statistics
+ This metapackage will install packages which are helpful to do statistics
+ with a special focus on tasks in medical care.
+
+Package: med-tools
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cycle, hunspell-de-med, mencal, pondus, quitcount, wgerman-medical
+Suggests: cl-pubmed, edfbrowser, hunspell-en-med, linuxorg-pcal, mssstest, python-clips
+Description: Debian Med several tools
+ This metapackage will install tools for several purposes in health care.
+ Currently it contains some simple programs for Personal Health.
+
+Package: med-typesetting
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: texlive-latex-extra, texlive-science
+Suggests: bibus, kbibtex
+Description: Debian Med support for typesetting and publishing
+ This metapackage will install Debian packages that might be helpful
+ for typesetting and publishing in medical care and structural
+ biology.
+
Added: projects/med/tags/1.5/debian/control
URL: http://svn.debian.org/wsvn/blends/projects/med/tags/1.5/debian/control?rev=3436&op=file
==============================================================================
--- projects/med/tags/1.5/debian/control (added)
+++ projects/med/tags/1.5/debian/control Sat Jun 23 12:46:46 2012
@@ -1,0 +1,192 @@
+# This file is autogenerated via make -f debian/rules dist. Do not edit!
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends-Indep: blends-dev (>= 0.6.9)
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/blends/projects/med/trunk/debian-med/
+
+Package: med-tasks
+Architecture: all
+Depends: tasksel
+Description: Debian Med tasks for tasksel
+ This package provides Debian Med tasks in tasksel.
+ .
+ These tasks are described in detail at
+ http://debian-med.alioth.debian.org/tasks/
+
+Package: med-config
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.9)
+Conflicts: med-common
+Replaces: med-common
+Provides: med-common
+Description: Debian Med Project config package
+ This package provides the basic infrastructure of all med-* packages and is
+ needed by them.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med using debconf.
+ .
+ Other packages in Debian Med Project are:
+ .
+ * med-bio for biological research
+ * med-bio-dev for developing applications in biological research
+ * med-cms for publicating a medical site on the internet
+ * med-epi for epidemiology
+ * med-imaging for image processing
+ * med-imaging-dev for developing applications for image processing
+ * med-pharmacy for pharmaceutical research
+ * med-physics for radiation oncology, diagnostic imaging, related fields
+ * med-practice for general practitioners
+ * med-tools contains miscellaneous tools
+ * med-typesetting depends from useful tools for typesetting
+ .
+ Note: All these packages are so called metapackages. This means they are not
+ executable programs, but only links to other packages. This way you will
+ conveniently get all the non-commercial medical software which is available
+ for Debian GNU/Linux.
+
+
+Package: med-bio
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: adun.app, alien-hunter, altree, amap-align, autodock, ballview, blast2, boxshade, bwa, dialign, dialign-tx, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, gamgi, garlic, gdpc, gff2aplot, gff2ps, ghemical, glam2, gromacs, hmmer, infernal, kalign, last-align, loki, mafft, maq, massxpert, melting, mipe, mummer, muscle, mustang, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, njplot, perlprimer, phyml, plasmidomics, poa, primer3, probcons, proda, pymol, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, readseq, rnahybrid, samtools, seaview, sibsim4, sigma-align, sim4, ssake, staden-io-lib-utils, t-coffee, theseus, tigr-glimmer, tree-puzzle | tree-ppuzzle, treeviewx, velvet, wise
+Suggests: acedb-other, acedb-other-belvu, acedb-other-dotter, act, agdbnet, amos-assembler, amoscmp, arb, artemis, asap, autodocktools, axparafit, axpcoords, bambus, beast-mcmc, big-blast, bio-mauve, blixem, bowtie, btk-core, cactus, caftools, cap3, cd-hit, cdna-db, clustalw, clustalw-mpi, clustalx, cluster3, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cytoscape, das-proserver, dazzle, decipher, dotter, dotur, ecell, elph, embassy-phylip, emboss-explorer, emboss-kaptain, est-db, estferret, estscan, exalt, excavator, fasta, fastx-toolkit, figaro, finex, fluctuate, forester, galaxy, gbioseq, gbrowse, genesplicer, genetrack, genezilla, genographer, glimmerhmm, gmv, grogui, haploview, hawkeye, hexamer, jalview, jigsaw, jmol, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, martj, mauvealigner, maxd, melting-gui, meme, mesquite, migrate, minimus, mira, mirbase, molekel, molphy, mozilla-biofox, mrbayes, msatfinder, mummergpu, murasaki, mview, ncoils, ngila, obo-edit, oligoarrayaux, omegamap, operondb, paml, partigene, patman, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phylip, phylographer, phylowin, plink, populations, prank, proalign, profit, prot4est, pyrophosphate-tools, qtlcart, r-ape, r-other-genabel, raster3d, raxml, rbs-finder, recombine, repeatfinder, reputer, roche454ace2caf, rose, rosetta, seq-gen, seqan-apps, sequenceconverter.app, smile, spice, splitstree, ssaha, tacg, taverna, taxinspector, tetra, tigr-assembler, tm-align, trace2dbest, tracetuner, transtermhp, treebuilder3d, treeplot, treevolve, trnascan-se, twain, uniprime, vienna-rna, wgs-assembler
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+
+Package: med-bio-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-primerdesigner-perl, libbio-ruby, libbiojava-java, libgenome-1.3-0-dev, libgo-perl, libncbi6-dev, libqsearch-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, mcl, octave-bioinfo, python-biopython, r-cran-genetics, r-cran-haplo.stats, seqan-dev
+Suggests: bioclipse, bioconductor, libajax5-dev, libbio-das-perl, libbio-mage-utils-perl, libbiococoa-dev, libgff-perl, libmems-1.5-1, libnucleus5-dev, libsbml1, limma, r-cran-rocr
+Description: Debian Med packages for development of micro-biology applications
+ This metapackage will install Debian packages which might be helpful
+ for development of applications for micro-biological research.
+
+Package: med-cms
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Suggests: zope-zms
+Description: Debian Med content management systems
+ This metapackage will install packages which are useful to build a
+ content management system for medical care.
+
+Package: med-epi
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: epigrass, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epitools
+Suggests: netepi-analysis, netepi-collection, r-cran-diagnosismed, r-cran-epir, r-cran-msm, r-cran-surveillance
+Description: Debian Med epidemiology related packages
+ This metapackage will install tools that are useful in epidemiological
+ research. Several packages making use of the GNU R data language for
+ statistical investigation. It might be a good idea to read the paper
+ "A short introduction to R for Epidemiology" at
+ http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
+
+Package: med-imaging
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, amide, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, fslview, gwyddion, imagej, libgdcm-tools, lipsia, medcon, minc-tools, nifti-bin, odin, python-mvpa, python-nifti, python-nipy, slicer, sofa-apps, via-bin, xmedcon
+Suggests: afni, bioimagesuite, blox, brainvisa, caret, cdmedicpacs, conquest-dicom-server, dcm4che, devide, dicom4j, drjekyll, ecg2png, fiji, fsl, imagemagick, imview, kradview, libvista2, maris, mesa-test-tools, micromanager, mni-autoreg, mni-n3, mrisim, opendicom.net, openelectrophy, opensourcepacs, piano, pixelmed, pixelmed-dicom-toolkit, pngquant, python-nipype, stir, visit
+Description: Debian Med imaging packages
+ This metapackage will install Debian packages which might be useful in
+ medical image processing.
+ .
+ It installs several packages supporting DICOM (Digital Imaging and
+ Communications in Medicine) which is the de-facto standard for medical
+ image management. The standard defines data structures and services for
+ the exchange of medical images and related information. The latest release
+ has been published in 2008 and consists of 18 parts.
+ .
+ For more information, you can visit the NEMA homepage
+ http://medical.nema.org/ .
+ .
+ The status of the official DICOM base standard plus all the
+ supplements and correction items are summarized at David Clunie's webpage:
+ http://www.dclunie.com/dicom-status/status.html
+ where you'll find direct links to the most recent yearly edition
+ ftp://medical.nema.org/medical/dicom/2008/ .
+
+Package: med-imaging-dev
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cimg-dev, ctn-dev, libcv-dev, libgdcm2-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti1-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-mvpa, python-nipy
+Suggests: gmic, igstk-examples, insighttoolkit3-examples, libigstk3-dev, libmni-perllib-perl, libnifti-doc, libvista2-dev, libvtk5, python-libavg, python-nipype, rumba
+Description: Debian Med packages for medical image development
+ This metapackage will install Debian packages which might be useful
+ for developing applications for medical image processing.
+
+Package: med-pharmacy
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: chemtool
+Description: Debian Med packages for pharmaceutical research
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research.
+
+Package: med-physics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: octave3.2, paw, paw++, r-base | r-base-core
+Suggests: biosig, gate, paw-demos
+Description: Debian Med packages for medical physicists
+ This metapackage contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields.
+
+Package: med-practice
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: aeskulap, gnumed-client, gnumed-server, libchipcard-tools
+Suggests: clearhealth, edfbrowser, elementalclinic, elexis, freeb, freemed, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, resmedicinae, sqlclinic, tinyheb
+Description: Debian Med packages for practice management
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for practitioners to manage their practice.
+
+Package: med-psychology
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: praat, psignifit, psychopy, python-pyepl, r-cran-foreign, r-cran-psy
+Suggests: visionegg
+Description: Debian Med packages for psychology
+ This metapackage contains dependencies for a collection of software
+ which might be helpful for psychological research.
+
+Package: med-statistics
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: r-cran-qvalue, r-cran-randomforest
+Suggests: science-statistics
+Description: Debian Med statistics
+ This metapackage will install packages which are helpful to do statistics
+ with a special focus on tasks in medical care.
+
+Package: med-tools
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: cycle, hunspell-de-med, mencal, pondus, quitcount, wgerman-medical
+Suggests: cl-pubmed, edfbrowser, hunspell-en-med, linuxorg-pcal, mssstest, python-clips
+Description: Debian Med several tools
+ This metapackage will install tools for several purposes in health care.
+ Currently it contains some simple programs for Personal Health.
+
+Package: med-typesetting
+Architecture: all
+Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
+Recommends: texlive-latex-extra, texlive-science
+Suggests: bibus, kbibtex
+Description: Debian Med support for typesetting and publishing
+ This metapackage will install Debian packages that might be helpful
+ for typesetting and publishing in medical care and structural
+ biology.
+
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