[Blends-commit] r1788 - projects/med/trunk/debian-med/tasks

Tue Aug 18 14:30:54 UTC 2009

Author: moeller
Date: Tue Aug 18 14:30:54 2009
New Revision: 1788
URL: http://svn.debian.org/viewsvn/blends?rev=1788&view=rev

Log:
ballview and r-other-mott-happy are now in Debian.


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1788&view=diff&r1=1788&r2=1787&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Aug 18 14:30:54 2009
@@ -121,26 +121,6 @@
  profiles and other state data.  Additional features are available as plugins.
 
 Recommends: ballview
-Homepage: http://www.ballview.org
-Responsible: Andreas Hildebrandt <anhi at bioinf.uni-sb.de>
-Pkg-URL: http://ftp-master.debian.org/new/ball_1.3+beta2.1-2.html
-WNPP: 407665
-License: LGPL
-Pkg-Description: free molecular modeling and molecular graphics tool
- BALLView provides fast OpenGL-based visualization of molecular structures,
- molecular mechanics methods (minimization, MD simulation using the
- AMBER, CHARMM, and MMFF94 force fields), calculation and visualization
- of electrostatic properties (FDPB) and molecular editing features.
- .
- BALLView is based on BALL (Biochemical Algorithms Library) ,
- which is currently being developed in the groups of Hans-Peter Lenhof
- (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher
- (University of Tuebingen, Germany). BALL is an application framework
- in C++ that has been specifically designed for rapid software
- development in Molecular Modeling and Computational Molecular Biology.
- It provides an extensive set of data structures as well as classes
- for Molecular Mechanics, advanced solvation methods, comparison and
- analysis of protein structures, file import/export, and visualization.
 
 Recommends: raxml
 Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
@@ -2212,49 +2192,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Recommends: r-happy
-Homepage: http://www.well.ox.ac.uk/happy/
-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: Multipoint QTL Mapping in Genetically Heterogeneous Animals
- Most phenotypes of medical importance can be measured quantitatively,
- and in many cases the genetic contribution is substantial, accounting
- for 40% or more of the phenotypic variance. Considerable efforts have
- been made to isolate the genes responsible for quantitative genetic
- variation in human populations, but with little success, mostly
- because genetic loci contributing to quantitative traits
- (quantitative trait loci, QTL) have only a small effect on the
- phenotype. Association studies have been proposed as the most
- appropriate method for finding the genes that influence complex
- traits. However, family-based studies may not provide the resolution
- needed for positional cloning, unless they are very large, while
- environmental or genetic differences between cases and controls may
- confound population-based association studies.
- .
- These difficulties have led to the study of animal models of human
- traits. Studies using experimental crosses between inbred animal
- strains have been successful in mapping QTLs with effects on a number
- of different phenotypes, including behaviour, but attempts to
- fine-map QTLs in animals have often foundered on the discovery that a
- single QTL of large effect was in fact due to multiple loci of small
- effect positioned within the same chromosomal region. A further
- potential difficulty with detecting QTLs between inbred crosses is
- the significant reduction in genetic heterogeneity compared to the
- total genetic variation present in animal populations: a QTL
- segregating in the wild need not be present in the experimental
- cross.
- .
- HAPPY was written to find QTLs in HS animals. It uses a multipoint
- analysis which offers significant improvements in statistical power
- to detect QTLs over that achieved by single-marker
- association. Further details can be found in
- Proc. Natl. Acad. Sci. USA, 10.1073/pnas.230304397.
-Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
- contains a happy package which seems to be the version in C which
- depends from the non-free NAG library.  We should package the R based
- version available at http://www.well.ox.ac.uk/happy/happyR.shtml
- which is entirely free.
+Recommends: r-other-mott-happy
 
 Recommends: jalview
 Homepage: http://www.jalview.org/

