[med-svn] r5530 - in trunk/community/papers: . 05_biomed_bio
Andreas Tille
tille at alioth.debian.org
Fri Dec 3 09:41:04 UTC 2010
Author: tille
Date: 2010-12-03 09:41:04 +0000 (Fri, 03 Dec 2010)
New Revision: 5530
Added:
trunk/community/papers/05_biomed_bio/
trunk/community/papers/05_biomed_bio/Makefile
trunk/community/papers/05_biomed_bio/README
trunk/community/papers/05_biomed_bio/acm_proc_article-sp.cls
trunk/community/papers/05_biomed_bio/debian-med-bio-llncs.tex
trunk/community/papers/05_biomed_bio/debian-med-bio.bib
trunk/community/papers/05_biomed_bio/debian-med-bio.tex
trunk/community/papers/05_biomed_bio/earthkeyring.png
trunk/community/papers/05_biomed_bio/llncs.cls
trunk/community/papers/05_biomed_bio/paper-text.tex
trunk/community/papers/05_biomed_bio/splncs.bst
Log:
Moved paper from Blends to Debian Med SVN
Added: trunk/community/papers/05_biomed_bio/Makefile
===================================================================
--- trunk/community/papers/05_biomed_bio/Makefile (rev 0)
+++ trunk/community/papers/05_biomed_bio/Makefile 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,101 @@
+#!/usr/bin/make -f
+
+text=debian-med-bio
+
+DISTDIR=debian-bio-0.2
+
+%.html: %.tex
+ echo "Unfortunately there is no latex 2 html solution for the moment."
+
+all: pdf
+# html dvi
+
+html: $(text).html
+$(text).html: $(text).tex
+ make clean
+ make bbl
+ cp -a $(text).tex $(text).tex.save
+ sed -i \
+ -e "s/\(\\documentclass{\)acm_proc_article-sp/\1article/" \
+ -e "s/\(\\\\titlenote{.*\)\\\\printurl{[^}]*}{[^}]*}/\1/" \
+ -e "/\\\\titlenote{/{;N;N;s/\\\\titlenote{[^}]*}//;}" \
+ -e "/\\\\affaddr{.*}/d" \
+ -e "/\\\\email{.*}/d" \
+ -e "/\\\\alignauthor/d" \
+ -e "/\\\\numberofauthors/d" \
+ $(text).tex
+ sed -i \
+ -e "/\\\\author{/{;N;N;N;N;N;N;N;N;s/\\\\author{[^}]*}//;}" \
+ -e "s/\\\\halfsloppy//" \
+ -e "/\\\\printurl/{;N;N;s?\\\\printurl{\([^}]*\)}\({[^}]*}\)?\\\\htmladdnormallink\2{http://\1}?g;}" \
+ -e "s/\(\\\\begin{tabular}{.*\)p{[^}]*}\(.*\)/\1l\2/" \
+ -e "/\\\\conferenceinfo/{;N;N;s/\\\\conferenceinfo{[^}]*}{[^}]*}/\\\\htmladdnormallink{Find the paper in PDF and more information about the conference here}{..}/;}" \
+ -e "s/\\\\CopyrightYear{[^}]*}//" \
+ $(text).tex
+ sed -i \
+ -e "/\\\\ifshowURL/{;N;N;N;s?\\\\ifshowURL.*|\(http://[^,]*\)[[:space:],]*\(http://[^|]*\)|}\\\\fi?\\\\htmladdnormallink{\1}{\1}, \\\\htmladdnormallink{\2}{\2}?g;}" \
+ $(text).bbl
+ sed -i \
+ -e "/\\\\ifshowURL/{;N;N;N;s?\\\\ifshowURL.*|\(http://[^|]*\)|}%*[[:space:]]*\\\\fi?\\\\htmladdnormallink{\1}{\1}?g;}" \
+ $(text).bbl
+ sed -i \
+ -e "/\\\\ifshowURL/{;N;N;s?\\\\ifshowURL.*|\(http://[^|]*\)|}%*[[:space:]]*\\\\fi?\\\\htmladdnormallink{\1}{\1}?g;}" \
+ -e "/\\\\htmladdnormallink/s/%/\\\\%/g" \
+ $(text).bbl
+ sed -i \
+ -e "/\\\\ifx[[:space:]]\\\\.*[[:space:]]\\\\fi/d" \
+ $(text).bbl
+ latex2html -local_icons $(text).tex
+ touch $(text).html
+ ##mv $(text).tex $(text).tex_used4html
+ mv $(text).tex.save $(text).tex
+
+bbl: $(text).bib
+ pdflatex $(text).tex
+ bibtex debian-med-bio
+
+dvi: $(text).dvi
+$(text).dvi: $(text).tex
+ make clean
+ convert earthkeyring.png earthkeyring.eps
+ latex $(text).tex
+ bibtex $(text)
+ latex $(text).tex
+ latex $(text).tex
+
+pdf: $(text).pdf
+$(text).pdf: $(text).tex paper-text.tex $(text).bib
+ make clean
+ pdflatex $(text).tex
+ bibtex $(text)
+ pdflatex $(text).tex
+ pdflatex $(text).tex
+
+pdfllncs: $(text)-llncs.pdf
+$(text)-llncs.pdf: $(text)-llncs.tex paper-text.tex
+ make clean
+ pdflatex $(text)-llncs.tex
+ bibtex $(text)-llncs
+ pdflatex $(text)-llncs.tex
+ pdflatex $(text)-llncs.tex
+
+dvips: $(text)-dvips.pdf
+$(text)-dvips.pdf: $(text).dvi
+ dvips -o $(text)-dvips.ps $(text).dvi
+ ps2pdf $(text)-dvips.ps
+ rm $(text)-dvips.ps
+
+distclean: clean
+ rm -f $(text)*.html $(text).pdf $(text)-dvips.pdf $(text)-llncs.pdf
+ rm -rf $(DISTDIR) debian-med-bio
+
+clean:
+ rm -f $(text)*.log $(text)*.aux $(text)*.dvi $(text)*.toc $(text)*.out $(text)*.bbl $(text)*.blg
+ rm -f *.log
+ rm -f earthkeyring.eps
+
+dist:
+ mkdir -p $(DISTDIR)/paper
+ cp -a *.tex *.css Makefile $(DISTDIR)/paper
+ tar -czf $(DISTDIR).tgz $(DISTDIR)
+ rm -rf $(DISTDIR)
Added: trunk/community/papers/05_biomed_bio/README
===================================================================
--- trunk/community/papers/05_biomed_bio/README (rev 0)
+++ trunk/community/papers/05_biomed_bio/README 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,24 @@
+You can download the necessary style for the proceeding at
+
+ http://www.acm.org/sigs/pubs/proceed/template.html
+
+The original submission to the AAMAS workshop 2005 at which this talk
+was presented utilised the following files with respect to the information
+presented in the aforementioned template description.
+
+ #wget http://www.acm.org/sigs/pubs/proceed/sig-alternate.cls
+ wget http://www.acm.org/sigs/pubs/proceed/acm_proc_article-sp.cls
+
+The BibTeX style which is able to handle URLs nicely is available by
+ wget ftp://ftp.math.utah.edu/pub/tex/bibtex/is-abbrv.bst
+
+For the publication at springeronline you have to use a different style
+named llncs2e which can be downloaded from
+ http://www.springer.de/comp/lncs/authors.html
+under the topic
+ Information for LNCS Authors --> Springer Author Discount
+which is named llncs2e.zip.
+The exact URL of the ZIP file is:
+ http://www.springeronline.com/sgw/cda/pageitems/document/cda_downloaddocument/0,11996,0-0-45-72895-0,00.zip
+
+
\ No newline at end of file
Added: trunk/community/papers/05_biomed_bio/acm_proc_article-sp.cls
===================================================================
--- trunk/community/papers/05_biomed_bio/acm_proc_article-sp.cls (rev 0)
+++ trunk/community/papers/05_biomed_bio/acm_proc_article-sp.cls 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,1391 @@
+% ACM_PROC_ARTICLE-SP.CLS - VERSION 2.7SP
+% COMPATIBLE WITH THE "ACM_PROC_ARTICLE.CLS" V2.5
+% Gerald Murray October 15th., 2004
+%
+% ---- Start of 'updates' ----
+%
+% Allowance made to switch default fonts between those systems using
+% METAFONT and those using 'Type 1' or 'Truetype' fonts.
+% See LINE NUMBER 266 for details.
+% Also provided for enumerated/annotated Corollaries 'surrounded' by
+% enumerated Theorems (line 838).
+% Gerry November 11th. 1999
+%
+% Made the Permission Statement / Conference Info / Copyright Info
+% 'user definable' in the source .tex file OR automatic if
+% not specified.
+% This 'sp' version does NOT produce the permission block.
+%
+% Major change in January 2000 was to include a "blank line" in between
+% new paragraphs. This involved major changes to the, then, acmproc-sp.cls 1.0SP
+% file, precipitating a 'new' name: "acm_proc_article-sp.cls" V2.01SP.
+%
+% Georgia fixed bug in sub-sub-section numbering in paragraphs (July 29th. 2002)
+% JS/GM fix to vertical spacing before Proofs (July 30th. 2002)
+%
+% Footnotes inside table cells using \minipage (Oct. 2002)
+%
+% ---- End of 'updates' ----
+%
+\def\fileversion{V2.7SP} % for ACM's tracking purposes
+\def\filedate{October 15, 2004} % Gerry Murray's tracking data
+\def\docdate {Friday 15th. October 2004} % Gerry Murray (with deltas to doc}
+\usepackage{epsfig}
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{amsfonts}
+%
+% ACM_PROC_ARTICLE-SP DOCUMENT STYLE
+% G.K.M. Tobin August-October 1999
+% adapted from ARTICLE document style by Ken Traub, Olin Shivers
+% also using elements of esub2acm.cls
+% LATEST REVISION V2.7SP - OCTOBER 2004
+% ARTICLE DOCUMENT STYLE -- Released 16 March 1988
+% for LaTeX version 2.09
+% Copyright (C) 1988 by Leslie Lamport
+%
+%
+%%% ACM_PROC_ARTICLE-SP is a document style for producing two-column camera-ready pages for
+%%% ACM conferences, according to ACM specifications. The main features of
+%%% this style are:
+%%%
+%%% 1) Two columns.
+%%% 2) Side and top margins of 4.5pc, bottom margin of 6pc, column gutter of
+%%% 2pc, hence columns are 20pc wide and 55.5pc tall. (6pc =3D 1in, approx)
+%%% 3) First page has title information, and an extra 6pc of space at the
+%%% bottom of the first column for the ACM copyright notice.
+%%% 4) Text is 9pt on 10pt baselines; titles (except main) are 9pt bold.
+%%%
+%%%
+%%% There are a few restrictions you must observe:
+%%%
+%%% 1) You cannot change the font size; ACM wants you to use 9pt.
+%%% 3) You must start your paper with the \maketitle command. Prior to the
+%%% \maketitle you must have \title and \author commands. If you have a
+%%% \date command it will be ignored; no date appears on the paper, since
+%%% the proceedings will have a date on the front cover.
+%%% 4) Marginal paragraphs, tables of contents, lists of figures and tables,
+%%% and page headings are all forbidden.
+%%% 5) The `figure' environment will produce a figure one column wide; if you
+%%% want one that is two columns wide, use `figure*'.
+%%%
+%
+%%% Copyright Space:
+%%% This style automatically leaves 1" blank space at the bottom of page 1/
+%%% column 1. This space can optionally be filled with some text using the
+%%% \toappear{...} command. If used, this command must be BEFORE the \maketitle
+%%% command. If this command is defined AND [preprint] is on, then the
+%%% space is filled with the {...} text (at the bottom); otherwise, it is
+%%% blank. If you use \toappearbox{...} instead of \toappear{...} then a
+%%% box will be drawn around the text (if [preprint] is on).
+%%%
+%%% A typical usage looks like this:
+%%% \toappear{To appear in the Ninth AES Conference on Medievil Lithuanian
+%%% Embalming Technique, June 1991, Alfaretta, Georgia.}
+%%% This will be included in the preprint, and left out of the conference
+%%% version.
+%%%
+%%% WARNING:
+%%% Some dvi-ps converters heuristically allow chars to drift from their
+%%% true positions a few pixels. This may be noticeable with the 9pt sans-serif
+%%% bold font used for section headers.
+%%% You may turn this hackery off via the -e option:
+%%% dvips -e 0 foo.dvi >foo.ps
+%%%
+\typeout{Document Class 'acm_proc_article-sp' <15th. October '04>. Modified by G.K.M. Tobin}
+\typeout{Based in part upon document Style `acmconf' <22 May 89>. Hacked 4/91 by}
+\typeout{shivers at cs.cmu.edu, 4/93 by theobald at cs.mcgill.ca}
+\typeout{Excerpts were taken from (Journal Style) 'esub2acm.cls'.}
+\typeout{****** Bugs/comments/suggestions to Gerry Murray -- murray at hq.acm.org ******}
+
+\oddsidemargin 4.5pc
+\evensidemargin 4.5pc
+\advance\oddsidemargin by -1in % Correct for LaTeX gratuitousness
+\advance\evensidemargin by -1in % Correct for LaTeX gratuitousness
+\marginparwidth 0pt % Margin pars are not allowed.
+\marginparsep 11pt % Horizontal space between outer margin and
+ % marginal note
+
+ % Top of page:
+\topmargin 4.5pc % Nominal distance from top of page to top of
+ % box containing running head.
+\advance\topmargin by -1in % Correct for LaTeX gratuitousness
+\headheight 0pt % Height of box containing running head.
+\headsep 0pt % Space between running head and text.
+ % Bottom of page:
+\footskip 30pt % Distance from baseline of box containing foot
+ % to baseline of last line of text.
+\@ifundefined{footheight}{\newdimen\footheight}{}% this is for LaTeX2e
+\footheight 12pt % Height of box containing running foot.
+
+
+%% Must redefine the top margin so there's room for headers and
+%% page numbers if you are using the preprint option. Footers
+%% are OK as is. Olin.
+\advance\topmargin by -37pt % Leave 37pt above text for headers
+\headheight 12pt % Height of box containing running head.
+\headsep 25pt % Space between running head and text.
+
+\textheight 666pt % 9 1/4 column height
+\textwidth 42pc % Width of text line.
+ % For two-column mode:
+\columnsep 2pc % Space between columns
+\columnseprule 0pt % Width of rule between columns.
+\hfuzz 1pt % Allow some variation in column width, otherwise it's
+ % too hard to typeset in narrow columns.
+
+\footnotesep 5.6pt % Height of strut placed at the beginning of every
+ % footnote =3D height of normal \footnotesize strut,
+ % so no extra space between footnotes.
+
+\skip\footins 8.1pt plus 4pt minus 2pt % Space between last line of text and
+ % top of first footnote.
+\floatsep 11pt plus 2pt minus 2pt % Space between adjacent floats moved
+ % to top or bottom of text page.
+\textfloatsep 18pt plus 2pt minus 4pt % Space between main text and floats
+ % at top or bottom of page.
+\intextsep 11pt plus 2pt minus 2pt % Space between in-text figures and
+ % text.
+\@ifundefined{@maxsep}{\newdimen\@maxsep}{}% this is for LaTeX2e
+\@maxsep 18pt % The maximum of \floatsep,
+ % \textfloatsep and \intextsep (minus
+ % the stretch and shrink).
+\dblfloatsep 11pt plus 2pt minus 2pt % Same as \floatsep for double-column
+ % figures in two-column mode.
+\dbltextfloatsep 18pt plus 2pt minus 4pt% \textfloatsep for double-column
+ % floats.
+\@ifundefined{@dblmaxsep}{\newdimen\@dblmaxsep}{}% this is for LaTeX2e
+\@dblmaxsep 18pt % The maximum of \dblfloatsep and
+ % \dbltexfloatsep.
+\@fptop 0pt plus 1fil % Stretch at top of float page/column. (Must be
+ % 0pt plus ...)
+\@fpsep 8pt plus 2fil % Space between floats on float page/column.
+\@fpbot 0pt plus 1fil % Stretch at bottom of float page/column. (Must be
+ % 0pt plus ... )
+\@dblfptop 0pt plus 1fil % Stretch at top of float page. (Must be 0pt plus ...)
+\@dblfpsep 8pt plus 2fil % Space between floats on float page.
+\@dblfpbot 0pt plus 1fil % Stretch at bottom of float page. (Must be
+ % 0pt plus ... )
+\marginparpush 5pt % Minimum vertical separation between two marginal
+ % notes.
+
+\parskip 0pt % Extra vertical space between paragraphs.
+ % Set to 0pt outside sections, to keep section heads
+ % uniformly spaced. The value of parskip is set
+ % to leading value _within_ sections.
+ % 12 Jan 2000 gkmt
+\parindent 0pt % Width of paragraph indentation.
+\partopsep 2pt plus 1pt minus 1pt% Extra vertical space, in addition to
+ % \parskip and \topsep, added when user
+ % leaves blank line before environment.
+
+\@lowpenalty 51 % Produced by \nopagebreak[1] or \nolinebreak[1]
+\@medpenalty 151 % Produced by \nopagebreak[2] or \nolinebreak[2]
+\@highpenalty 301 % Produced by \nopagebreak[3] or \nolinebreak[3]
+
+\@beginparpenalty -\@lowpenalty % Before a list or paragraph environment.
+\@endparpenalty -\@lowpenalty % After a list or paragraph environment.
+\@itempenalty -\@lowpenalty % Between list items.
+
+\@namedef{ds at 10pt}{\@latexerr{The `10pt' option is not allowed in the `acmconf'
+ document style.}\@eha}
+\@namedef{ds at 11pt}{\@latexerr{The `11pt' option is not allowed in the `acmconf'
+ document style.}\@eha}
+\@namedef{ds at 12pt}{\@latexerr{The `12pt' option is not allowed in the `acmconf'
+ document style.}\@eha}
+
+\@options
+
+\lineskip 2pt % \lineskip is 1pt for all font sizes.
+\normallineskip 2pt
+\def\baselinestretch{1}
+
+\abovedisplayskip 9pt plus2pt minus4.5pt%
+\belowdisplayskip \abovedisplayskip
+\abovedisplayshortskip \z@ plus3pt%
+\belowdisplayshortskip 5.4pt plus3pt minus3pt%
+\let\@listi\@listI % Setting of \@listi added 9 Jun 87
+
+\def\small{\@setsize\small{9pt}\viiipt\@viiipt
+\abovedisplayskip 7.6pt plus 3pt minus 4pt%
+\belowdisplayskip \abovedisplayskip
+\abovedisplayshortskip \z@ plus2pt%
+\belowdisplayshortskip 3.6pt plus2pt minus 2pt
+\def\@listi{\leftmargin\leftmargini %% Added 22 Dec 87
+\topsep 4pt plus 2pt minus 2pt\parsep 2pt plus 1pt minus 1pt
+\itemsep \parsep}}
+
+\def\footnotesize{\@setsize\footnotesize{9pt}\ixpt\@ixpt
+\abovedisplayskip 6.4pt plus 2pt minus 4pt%
+\belowdisplayskip \abovedisplayskip
+\abovedisplayshortskip \z@ plus 1pt%
+\belowdisplayshortskip 2.7pt plus 1pt minus 2pt
+\def\@listi{\leftmargin\leftmargini %% Added 22 Dec 87
+\topsep 3pt plus 1pt minus 1pt\parsep 2pt plus 1pt minus 1pt
+\itemsep \parsep}}
+
+\newcount\aucount
+\newcount\originalaucount
+\newdimen\auwidth
+\auwidth=\textwidth
+\newdimen\auskip
+\newcount\auskipcount
+\newdimen\auskip
+\global\auskip=1pc
+\newdimen\allauboxes
+\allauboxes=\auwidth
+\newtoks\addauthors
+\newcount\addauflag
+\global\addauflag=0 %Haven't shown additional authors yet
+
+\newtoks\subtitletext
+\gdef\subtitle#1{\subtitletext={#1}}
+
+\gdef\additionalauthors#1{\addauthors={#1}}
+
+\gdef\numberofauthors#1{\global\aucount=#1
+\ifnum\aucount>3\global\originalaucount=\aucount \global\aucount=3\fi %g}
+\global\auskipcount=\aucount\global\advance\auskipcount by 1
+\global\multiply\auskipcount by 2
+\global\multiply\auskip by \auskipcount
+\global\advance\auwidth by -\auskip
+\global\divide\auwidth by \aucount}
+
+% \and was modified to count the number of authors. GKMT 12 Aug 1999
+\def\alignauthor{% % \begin{tabular}
+\end{tabular}%
+ \begin{tabular}[t]{p{\auwidth}}\centering}%
+
+% *** NOTE *** NOTE *** NOTE *** NOTE ***
+% If you have 'font problems' then you may need
+% to change these, e.g. 'arialb' instead of "arialbd".
+% Gerry Murray 11/11/1999
+% *** OR ** comment out block A and activate block B or vice versa.
+% **********************************************
+%
+% -- Start of block A -- (Type 1 or Truetype fonts)
+%\newfont{\secfnt}{timesbd at 12pt} % was timenrb originally - now is timesbd
+%\newfont{\secit}{timesbi at 12pt} %13 Jan 00 gkmt
+%\newfont{\subsecfnt}{timesi at 11pt} % was timenrri originally - now is timesi
+%\newfont{\subsecit}{timesbi at 11pt} % 13 Jan 00 gkmt -- was times changed to timesbi gm 2/4/2000
+% % because "normal" is italic, "italic" is Roman
+%\newfont{\ttlfnt}{arialbd at 18pt} % was arialb originally - now is arialbd
+%\newfont{\ttlit}{arialbi at 18pt} % 13 Jan 00 gkmt
+%\newfont{\subttlfnt}{arial at 14pt} % was arialr originally - now is arial
+%\newfont{\subttlit}{ariali at 14pt} % 13 Jan 00 gkmt
+%\newfont{\subttlbf}{arialbd at 14pt} % 13 Jan 00 gkmt
+%\newfont{\aufnt}{arial at 12pt} % was arialr originally - now is arial
+%\newfont{\auit}{ariali at 12pt} % 13 Jan 00 gkmt
+%\newfont{\affaddr}{arial at 10pt} % was arialr originally - now is arial
+%\newfont{\affaddrit}{ariali at 10pt} %13 Jan 00 gkmt
+%\newfont{\eaddfnt}{arial at 12pt} % was arialr originally - now is arial
+%\newfont{\ixpt}{times at 9pt} % was timenrr originally - now is times
+%\newfont{\confname}{timesi at 8pt} % was timenrri - now is timesi
+%\newfont{\crnotice}{times at 8pt} % was timenrr originally - now is times
+%\newfont{\ninept}{times at 9pt} % was timenrr originally - now is times
+
+% *********************************************
+% -- End of block A --
+%
+%
+% -- Start of block B -- METAFONT
+% +++++++++++++++++++++++++++++++++++++++++++++
+% Next (default) block for those using Metafont
+% Gerry Murray 11/11/1999
+% *** THIS BLOCK FOR THOSE USING METAFONT *****
+% *********************************************
+\newfont{\secfnt}{ptmb at 12pt}
+\newfont{\secit}{ptmbi at 12pt} %13 Jan 00 gkmt
+\newfont{\subsecfnt}{ptmri at 11pt}
+\newfont{\subsecit}{ptmbi at 11pt} % 13 Jan 00 gkmt -- was ptmr changed to ptmbi gm 2/4/2000
+ % because "normal" is italic, "italic" is Roman
+\newfont{\ttlfnt}{phvb at 18pt}
+\newfont{\ttlit}{phvbo at 18pt} % GM 2/4/2000
+\newfont{\subttlfnt}{phvr at 14pt}
+\newfont{\subttlit}{phvro at 14pt} % GM 2/4/2000
+\newfont{\subttlbf}{phvb at 14pt} % 13 Jan 00 gkmt
+\newfont{\aufnt}{phvr at 12pt}
+\newfont{\auit}{phvro at 12pt} % GM 2/4/2000
+\newfont{\affaddr}{phvr at 10pt}
+\newfont{\affaddrit}{phvro at 10pt} % GM 2/4/2000
+\newfont{\eaddfnt}{phvr at 12pt}
+\newfont{\ixpt}{ptmr at 9pt}
+\newfont{\confname}{ptmri at 8pt}
+\newfont{\crnotice}{ptmr at 8pt}
+\newfont{\ninept}{ptmr at 9pt}
+% +++++++++++++++++++++++++++++++++++++++++++++
+% -- End of block B --
+
+\def\email#1{{{\eaddfnt{\vskip 4pt#1}}}}
+
+\def\addauthorsection{\ifnum\originalaucount>3
+ \section{Additional Authors}\the\addauthors
+ \fi}
+
+\newcount\savesection
+\newcount\sectioncntr
+\global\sectioncntr=1
+
+\setcounter{secnumdepth}{3}
+
+\def\appendix{\par
+\section*{APPENDIX}
+\setcounter{section}{0}
+ \setcounter{subsection}{0}
+ \def\thesection{\Alph{section}} }
+
+
+\leftmargini 22.5pt
+\leftmarginii 19.8pt % > \labelsep + width of '(m)'
+\leftmarginiii 16.8pt % > \labelsep + width of 'vii.'
+\leftmarginiv 15.3pt % > \labelsep + width of 'M.'
+\leftmarginv 9pt
+\leftmarginvi 9pt
+
+\leftmargin\leftmargini
+\labelsep 4.5pt
+\labelwidth\leftmargini\advance\labelwidth-\labelsep
+
+\def\@listI{\leftmargin\leftmargini \parsep 3.6pt plus 2pt minus 1pt%
+\topsep 7.2pt plus 2pt minus 4pt%
+\itemsep 3.6pt plus 2pt minus 1pt}
+
+\let\@listi\@listI
+\@listi
+
+\def\@listii{\leftmargin\leftmarginii
+ \labelwidth\leftmarginii\advance\labelwidth-\labelsep
+ \topsep 3.6pt plus 2pt minus 1pt
+ \parsep 1.8pt plus 0.9pt minus 0.9pt
+ \itemsep \parsep}
+
+\def\@listiii{\leftmargin\leftmarginiii
+ \labelwidth\leftmarginiii\advance\labelwidth-\labelsep
+ \topsep 1.8pt plus 0.9pt minus 0.9pt
+ \parsep \z@ \partopsep 1pt plus 0pt minus 1pt
+ \itemsep \topsep}
+
+\def\@listiv{\leftmargin\leftmarginiv
+ \labelwidth\leftmarginiv\advance\labelwidth-\labelsep}
+
+\def\@listv{\leftmargin\leftmarginv
+ \labelwidth\leftmarginv\advance\labelwidth-\labelsep}
+
+\def\@listvi{\leftmargin\leftmarginvi
+ \labelwidth\leftmarginvi\advance\labelwidth-\labelsep}
+
+\def\labelenumi{\theenumi.}
+\def\theenumi{\arabic{enumi}}
+
+\def\labelenumii{(\theenumii)}
+\def\theenumii{\alph{enumii}}
+\def\p at enumii{\theenumi}
+
+\def\labelenumiii{\theenumiii.}
+\def\theenumiii{\roman{enumiii}}
+\def\p at enumiii{\theenumi(\theenumii)}
+
+\def\labelenumiv{\theenumiv.}
+\def\theenumiv{\Alph{enumiv}}
+\def\p at enumiv{\p at enumiii\theenumiii}
+
+\def\labelitemi{$\bullet$}
+\def\labelitemii{\bf --}
+\def\labelitemiii{$\ast$}
+\def\labelitemiv{$\cdot$}
+
+\def\verse{\let\\=\@centercr
+ \list{}{\itemsep\z@ \itemindent -1.5em\listparindent \itemindent
+ \rightmargin\leftmargin\advance\leftmargin 1.5em}\item[]}
+\let\endverse\endlist
+
+\def\quotation{\list{}{\listparindent 1.5em
+ \itemindent\listparindent
+ \rightmargin\leftmargin \parsep 0pt plus 1pt}\item[]}
+\let\endquotation=\endlist
+
+\def\quote{\list{}{\rightmargin\leftmargin}\item[]}
+\let\endquote=\endlist
+
+\def\descriptionlabel#1{\hspace\labelsep \bf #1}
+\def\description{\list{}{\labelwidth\z@ \itemindent-\leftmargin
+ \let\makelabel\descriptionlabel}}
+
+\let\enddescription\endlist
+
+\def\theequation{\arabic{equation}}
+
+\arraycolsep 4.5pt % Half the space between columns in an array environment.
+\tabcolsep 5.4pt % Half the space between columns in a tabular environment.
+\arrayrulewidth .4pt % Width of rules in array and tabular environment.
+\doublerulesep 1.8pt % Space between adjacent rules in array or tabular env.
+
+\tabbingsep \labelsep % Space used by the \' command. (See LaTeX manual.)
+
+\skip\@mpfootins =\skip\footins
+
+\fboxsep =2.7pt % Space left between box and text by \fbox and \framebox.
+\fboxrule =.4pt % Width of rules in box made by \fbox and \framebox.
+
+\def\thepart{\Roman{part}} % Roman numeral part numbers.
+\def\thesection {\arabic{section}}
+\def\thesubsection {\thesection.\arabic{subsection}}
+%\def\thesubsubsection {\thesubsection.\arabic{subsubsection}} % GM 7/30/2002
+%\def\theparagraph {\thesubsubsection.\arabic{paragraph}} % GM 7/30/2002
+\def\thesubparagraph {\theparagraph.\arabic{subparagraph}}
+
+\def\@pnumwidth{1.55em}
+\def\@tocrmarg {2.55em}
+\def\@dotsep{4.5}
+\setcounter{tocdepth}{3}
+
+\def\tableofcontents{\@latexerr{\tableofcontents: Tables of contents are not
+ allowed in the `acmconf' document style.}\@eha}
+
+\def\l at part#1#2{\addpenalty{\@secpenalty}
+ \addvspace{2.25em plus 1pt} % space above part line
+ \begingroup
+ \@tempdima 3em % width of box holding part number, used by
+ \parindent \z@ \rightskip \@pnumwidth %% \numberline
+ \parfillskip -\@pnumwidth
+ {\large \bf % set line in \large boldface
+ \leavevmode % TeX command to enter horizontal mode.
+ #1\hfil \hbox to\@pnumwidth{\hss #2}}\par
+ \nobreak % Never break after part entry
+ \endgroup}
+
+\def\l at section#1#2{\addpenalty{\@secpenalty} % good place for page break
+ \addvspace{1.0em plus 1pt} % space above toc entry
+ \@tempdima 1.5em % width of box holding section number
+ \begingroup
+ \parindent \z@ \rightskip \@pnumwidth
+ \parfillskip -\@pnumwidth
+ \bf % Boldface.
+ \leavevmode % TeX command to enter horizontal mode.
+ \advance\leftskip\@tempdima %% added 5 Feb 88 to conform to
+ \hskip -\leftskip %% 25 Jan 88 change to \numberline
+ #1\nobreak\hfil \nobreak\hbox to\@pnumwidth{\hss #2}\par
+ \endgroup}
+
+
+\def\l at subsection{\@dottedtocline{2}{1.5em}{2.3em}}
+\def\l at subsubsection{\@dottedtocline{3}{3.8em}{3.2em}}
+\def\l at paragraph{\@dottedtocline{4}{7.0em}{4.1em}}
+\def\l at subparagraph{\@dottedtocline{5}{10em}{5em}}
+
+\def\listoffigures{\@latexerr{\listoffigures: Lists of figures are not
+ allowed in the `acmconf' document style.}\@eha}
+
+\def\l at figure{\@dottedtocline{1}{1.5em}{2.3em}}
+
+\def\listoftables{\@latexerr{\listoftables: Lists of tables are not
+ allowed in the `acmconf' document style.}\@eha}
+\let\l at table\l at figure
+
+\def\footnoterule{\kern-3\p@
+ \hrule width .4\columnwidth
+ \kern 2.6\p@} % The \hrule has default height of .4pt .
+% ------
+\long\def\@makefntext#1{\noindent
+%\hbox to .5em{\hss$^{\@thefnmark}$}#1} % original
+\hbox to .5em{\hss\textsuperscript{\@thefnmark}}#1} % C. Clifton / GM Oct. 2nd. 2002
+% -------
+
+\long\def\@maketntext#1{\noindent
+#1}
+
+\long\def\@maketitlenotetext#1#2{\noindent
+ \hbox to 1.8em{\hss$^{#1}$}#2}
+
+\setcounter{topnumber}{2}
+\def\topfraction{.7}
+\setcounter{bottomnumber}{1}
+\def\bottomfraction{.3}
+\setcounter{totalnumber}{3}
+\def\textfraction{.2}
+\def\floatpagefraction{.5}
+\setcounter{dbltopnumber}{2}
+\def\dbltopfraction{.7}
+\def\dblfloatpagefraction{.5}
+
+\long\def\@makecaption#1#2{
+ \vskip \baselineskip
+ \setbox\@tempboxa\hbox{\textbf{#1: #2}}
+ \ifdim \wd\@tempboxa >\hsize % IF longer than one line:
+ \textbf{#1: #2}\par % THEN set as ordinary paragraph.
+ \else % ELSE center.
+ \hbox to\hsize{\hfil\box\@tempboxa\hfil}\par
+ \fi}
+
+\@ifundefined{figure}{\newcounter {figure}} % this is for LaTeX2e
+
+\def\fps at figure{tbp}
+\def\ftype at figure{1}
+\def\ext at figure{lof}
+\def\fnum at figure{Figure \thefigure}
+\def\figure{\@float{figure}}
+\let\endfigure\end at float
+\@namedef{figure*}{\@dblfloat{figure}}
+\@namedef{endfigure*}{\end at dblfloat}
+
+\@ifundefined{table}{\newcounter {table}} % this is for LaTeX2e
+
+\def\fps at table{tbp}
+\def\ftype at table{2}
+\def\ext at table{lot}
+\def\fnum at table{Table \thetable}
+\def\table{\@float{table}}
+\let\endtable\end at float
+\@namedef{table*}{\@dblfloat{table}}
+\@namedef{endtable*}{\end at dblfloat}
+
+\newtoks\titleboxnotes
+\newcount\titleboxnoteflag
+
+\def\maketitle{\par
+ \begingroup
+ \def\thefootnote{\fnsymbol{footnote}}
+ \def\@makefnmark{\hbox
+ to 0pt{$^{\@thefnmark}$\hss}}
+ \twocolumn[\@maketitle]
+\@thanks
+ \endgroup
+ \setcounter{footnote}{0}
+ \let\maketitle\relax
+ \let\@maketitle\relax
+ \gdef\@thanks{}\gdef\@author{}\gdef\@title{}\gdef\@subtitle{}\let\thanks\relax
+ \@copyrightspace}
+
+%% CHANGES ON NEXT LINES
+\newif\if at ll % to record which version of LaTeX is in use
+
+\expandafter\ifx\csname LaTeXe\endcsname\relax % LaTeX2.09 is used
+\else% LaTeX2e is used, so set ll to true
+\global\@lltrue
+\fi
+
+\if at ll
+ \NeedsTeXFormat{LaTeX2e}
+ \ProvidesClass{acm_proc_article-sp} [2004/15/10 - V2.7SP - based on esub2acm.sty <23 April 96>]
+ \RequirePackage{latexsym}% QUERY: are these two really needed?
+ \let\dooptions\ProcessOptions
+\else
+ \let\dooptions\@options
+\fi
+%% END CHANGES
+
+\def\@height{height}
+\def\@width{width}
+\def\@minus{minus}
+\def\@plus{plus}
+\def\hb at xt@{\hbox to}
+\newif\if at faircopy
+\@faircopyfalse
+\def\ds at faircopy{\@faircopytrue}
+
+\def\ds at preprint{\@faircopyfalse}
+
+\@twosidetrue
+\@mparswitchtrue
+\def\ds at draft{\overfullrule 5\p@}
+%% CHANGE ON NEXT LINE
+\dooptions
+
+\lineskip \p@
+\normallineskip \p@
+\def\baselinestretch{1}
+\def\@ptsize{0} %needed for amssymbols.sty
+
+%% CHANGES ON NEXT LINES
+\if at ll% allow use of old-style font change commands in LaTeX2e
+\@maxdepth\maxdepth
+%
+\DeclareOldFontCommand{\rm}{\ninept\rmfamily}{\mathrm}
+\DeclareOldFontCommand{\sf}{\normalfont\sffamily}{\mathsf}
+\DeclareOldFontCommand{\tt}{\normalfont\ttfamily}{\mathtt}
+\DeclareOldFontCommand{\bf}{\normalfont\bfseries}{\mathbf}
+\DeclareOldFontCommand{\it}{\normalfont\itshape}{\mathit}
+\DeclareOldFontCommand{\sl}{\normalfont\slshape}{\@nomath\sl}
+\DeclareOldFontCommand{\sc}{\normalfont\scshape}{\@nomath\sc}
+\DeclareRobustCommand*{\cal}{\@fontswitch{\relax}{\mathcal}}
+\DeclareRobustCommand*{\mit}{\@fontswitch{\relax}{\mathnormal}}
+\fi
+%
+\if at ll
+ \renewcommand{\rmdefault}{cmr} % was 'ttm'
+% Note! I have also found 'mvr' to work ESPECIALLY well.
+% Gerry - October 1999
+% You may need to change your LV1times.fd file so that sc is
+% mapped to cmcsc - -for smallcaps -- that is if you decide
+% to change {cmr} to {times} above. (Not recommended)
+ \renewcommand{\@ptsize}{}
+ \renewcommand{\normalsize}{%
+ \@setfontsize\normalsize\@ixpt{10.5\p@}%\ninept%
+ \abovedisplayskip 6\p@ \@plus2\p@ \@minus\p@
+ \belowdisplayskip \abovedisplayskip
+ \abovedisplayshortskip 6\p@ \@minus 3\p@
+ \belowdisplayshortskip 6\p@ \@minus 3\p@
+ \let\@listi\@listI
+ }
+\else
+ \def\@normalsize{%changed next to 9 from 10
+ \@setsize\normalsize{9\p@}\ixpt\@ixpt
+ \abovedisplayskip 6\p@ \@plus2\p@ \@minus\p@
+ \belowdisplayskip \abovedisplayskip
+ \abovedisplayshortskip 6\p@ \@minus 3\p@
+ \belowdisplayshortskip 6\p@ \@minus 3\p@
+ \let\@listi\@listI
+ }%
+\fi
+\if at ll
+ \newcommand\scriptsize{\@setfontsize\scriptsize\@viipt{8\p@}}
+ \newcommand\tiny{\@setfontsize\tiny\@vpt{6\p@}}
+ \newcommand\large{\@setfontsize\large\@xiipt{14\p@}}
+ \newcommand\Large{\@setfontsize\Large\@xivpt{18\p@}}
+ \newcommand\LARGE{\@setfontsize\LARGE\@xviipt{20\p@}}
+ \newcommand\huge{\@setfontsize\huge\@xxpt{25\p@}}
+ \newcommand\Huge{\@setfontsize\Huge\@xxvpt{30\p@}}
+\else
+ \def\scriptsize{\@setsize\scriptsize{8\p@}\viipt\@viipt}
+ \def\tiny{\@setsize\tiny{6\p@}\vpt\@vpt}
+ \def\large{\@setsize\large{14\p@}\xiipt\@xiipt}
+ \def\Large{\@setsize\Large{18\p@}\xivpt\@xivpt}
+ \def\LARGE{\@setsize\LARGE{20\p@}\xviipt\@xviipt}
+ \def\huge{\@setsize\huge{25\p@}\xxpt\@xxpt}
+ \def\Huge{\@setsize\Huge{30\p@}\xxvpt\@xxvpt}
+\fi
+\normalsize
+
+% make aubox hsize/number of authors up to 3, less gutter
+% then showbox gutter showbox gutter showbox -- GKMT Aug 99
+\newbox\@acmtitlebox
+\def\@maketitle{\newpage
+ \null
+ \setbox\@acmtitlebox\vbox{%
+\baselineskip 20pt
+\vskip 2em % Vertical space above title.
+ \begin{center}
+ {\ttlfnt \@title\par} % Title set in 18pt Helvetica (Arial) bold size.
+ \vskip 1.5em % Vertical space after title.
+%This should be the subtitle.
+{\subttlfnt \the\subtitletext\par}\vskip 1.25em%\fi
+ {\baselineskip 16pt\aufnt % each author set in \12 pt Arial, in a
+ \lineskip .5em % tabular environment
+ \begin{tabular}[t]{c}\@author
+ \end{tabular}\par}
+ \vskip 1.5em % Vertical space after author.
+ \end{center}}
+ \dimen0=\ht\@acmtitlebox
+ \advance\dimen0 by -12.75pc\relax % Increased space for title box -- KBT
+ \unvbox\@acmtitlebox
+ \ifdim\dimen0<0.0pt\relax\vskip-\dimen0\fi}
+
+
+\newcount\titlenotecount
+\global\titlenotecount=0
+\newtoks\tntoks
+\newtoks\tntokstwo
+\newtoks\tntoksthree
+\newtoks\tntoksfour
+\newtoks\tntoksfive
+
+\def\abstract{
+\ifnum\titlenotecount>0 % was =1
+ \insert\footins{%
+ \reset at font\footnotesize
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\footnotesep
+ \splitmaxdepth \dp\strutbox \floatingpenalty \@MM
+ \hsize\columnwidth \@parboxrestore
+ \protected at edef\@currentlabel{%
+ }%
+ \color at begingroup
+\ifnum\titlenotecount=1
+ \@maketntext{%
+ \raisebox{4pt}{$\ast$}\rule\z@\footnotesep\ignorespaces\the\tntoks\@finalstrut\strutbox}%
+\fi
+\ifnum\titlenotecount=2
+ \@maketntext{%
+ \raisebox{4pt}{$\ast$}\rule\z@\footnotesep\ignorespaces\the\tntoks\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\dagger$}\rule\z@\footnotesep\ignorespaces\the\tntokstwo\@finalstrut\strutbox}%
+\fi
+\ifnum\titlenotecount=3
+ \@maketntext{%
+ \raisebox{4pt}{$\ast$}\rule\z@\footnotesep\ignorespaces\the\tntoks\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\dagger$}\rule\z@\footnotesep\ignorespaces\the\tntokstwo\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\ddagger$}\rule\z@\footnotesep\ignorespaces\the\tntoksthree\@finalstrut\strutbox}%
+\fi
+\ifnum\titlenotecount=4
+ \@maketntext{%
+ \raisebox{4pt}{$\ast$}\rule\z@\footnotesep\ignorespaces\the\tntoks\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\dagger$}\rule\z@\footnotesep\ignorespaces\the\tntokstwo\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\ddagger$}\rule\z@\footnotesep\ignorespaces\the\tntoksthree\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\S$}\rule\z@\footnotesep\ignorespaces\the\tntoksfour\@finalstrut\strutbox}%
+\fi
+\ifnum\titlenotecount=5
+ \@maketntext{%
+ \raisebox{4pt}{$\ast$}\rule\z@\footnotesep\ignorespaces\the\tntoks\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\dagger$}\rule\z@\footnotesep\ignorespaces\the\tntokstwo\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\ddagger$}\rule\z@\footnotesep\ignorespaces\the\tntoksthree\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\S$}\rule\z@\footnotesep\ignorespaces\the\tntoksfour\par\@finalstrut\strutbox}%
+\@maketntext{%
+ \raisebox{4pt}{$\P$}\rule\z@\footnotesep\ignorespaces\the\tntoksfive\@finalstrut\strutbox}%
+\fi
+ \color at endgroup} %g}
+\fi
+\setcounter{footnote}{0}
+\section*{ABSTRACT}\normalsize %\the\parskip \the\baselineskip%\ninept
+}
+
+\def\endabstract{\if at twocolumn\else\endquotation\fi}
+
+\def\keywords{\if at twocolumn
+\section*{Keywords}
+\else \small
+\quotation
+\fi}
+
+% I've pulled the check for 2 cols, since proceedings are _always_
+% two-column 11 Jan 2000 gkmt
+\def\terms{%\if at twocolumn
+\section*{General Terms}
+%\else \small
+%\quotation\the\parskip
+%\fi}
+}
+
+% -- Classification needs to be a bit smart due to optionals - Gerry/Georgia November 2nd. 1999
+\newcount\catcount
+\global\catcount=1
+
+\def\category#1#2#3{%
+\ifnum\catcount=1
+\section*{Categories and Subject Descriptors}
+\advance\catcount by 1\else{\unskip; }\fi
+ \@ifnextchar [{\@category{#1}{#2}{#3}}{\@category{#1}{#2}{#3}[]}%
+}
+
+\def\@category#1#2#3[#4]{%
+ \begingroup
+ \let\and\relax
+ #1 [\textbf{#2}]%
+ \if!#4!%
+ \if!#3!\else : #3\fi
+ \else
+ :\space
+ \if!#3!\else #3\kern\z at ---\hskip\z@\fi
+ \textit{#4}%
+ \fi
+ \endgroup
+}
+%
+
+%%% This section (written by KBT) handles the 1" box in the lower left
+%%% corner of the left column of the first page by creating a picture,
+%%% and inserting the predefined string at the bottom (with a negative
+%%% displacement to offset the space allocated for a non-existent
+%%% caption).
+%%%
+\newtoks\copyrightnotice
+\def\ftype at copyrightbox{8}
+\def\@copyrightspace{
+\@float{copyrightbox}[b]
+\begin{center}
+\setlength{\unitlength}{1pc}
+\begin{picture}(20,6) %Space for copyright notice
+\put(0,-0.95){\crnotice{\@toappear}}
+\end{picture}
+\end{center}
+\end at float}
+
+\def\@toappear{} % Default setting blank - commands below change this.
+\long\def\toappear#1{\def\@toappear{\parbox[b]{20pc}{\baselineskip 9pt#1}}}
+\def\toappearbox#1{\def\@toappear{\raisebox{5pt}{\framebox[20pc]{\parbox[b]{19pc}{#1}}}}}
+
+\newtoks\conf
+\newtoks\confinfo
+\def\conferenceinfo#1#2{\global\conf={#1}\global\confinfo{#2}}
+
+
+\def\marginpar{\@latexerr{The \marginpar command is not allowed in the
+ `acmconf' document style.}\@eha}
+
+\mark{{}{}} % Initializes TeX's marks
+
+\def\today{\ifcase\month\or
+ January\or February\or March\or April\or May\or June\or
+ July\or August\or September\or October\or November\or December\fi
+ \space\number\day, \number\year}
+
+\def\@begintheorem#1#2{%
+ \trivlist
+ \item[%
+ \hskip 10\p@
+ \hskip \labelsep
+ {{\sc #1}\hskip 5\p@\relax#2.}%
+ ]
+ \it
+}
+\def\@opargbegintheorem#1#2#3{%
+ \trivlist
+ \item[%
+ \hskip 10\p@
+ \hskip \labelsep
+ {\sc #1\ #2\ % This mod by Gerry to enumerate corollaries
+ \setbox\@tempboxa\hbox{(#3)} % and bracket the 'corollary title'
+ \ifdim \wd\@tempboxa>\z@ % and retain the correct numbering of e.g. theorems
+ \hskip 5\p@\relax % if they occur 'around' said corollaries.
+ \box\@tempboxa % Gerry - Nov. 1999.
+ \fi.}%
+ ]
+ \it
+}
+\newif\if at qeded
+\global\@qededfalse
+
+% -- original
+%\def\proof{%
+% \vspace{-\parskip} % GM July 2000 (for tighter spacing)
+% \global\@qededfalse
+% \@ifnextchar[{\@xproof}{\@proof}%
+%}
+% -- end of original
+
+% (JSS) Fix for vertical spacing bug - Gerry Murray July 30th. 2002
+\def\proof{%
+\vspace{-\lastskip}\vspace{-\parsep}\penalty-51%
+\global\@qededfalse
+\@ifnextchar[{\@xproof}{\@proof}%
+}
+
+\def\endproof{%
+ \if at qeded\else\qed\fi
+ \endtrivlist
+}
+\def\@proof{%
+ \trivlist
+ \item[%
+ \hskip 10\p@
+ \hskip \labelsep
+ {\sc Proof.}%
+ ]
+ \ignorespaces
+}
+\def\@xproof[#1]{%
+ \trivlist
+ \item[\hskip 10\p@\hskip \labelsep{\sc Proof #1.}]%
+ \ignorespaces
+}
+\def\qed{%
+ \unskip
+ \kern 10\p@
+ \begingroup
+ \unitlength\p@
+ \linethickness{.4\p@}%
+ \framebox(6,6){}%
+ \endgroup
+ \global\@qededtrue
+}
+
+\def\newdef#1#2{%
+ \expandafter\@ifdefinable\csname #1\endcsname
+ {\@definecounter{#1}%
+ \expandafter\xdef\csname the#1\endcsname{\@thmcounter{#1}}%
+ \global\@namedef{#1}{\@defthm{#1}{#2}}%
+ \global\@namedef{end#1}{\@endtheorem}%
+ }%
+}
+\def\@defthm#1#2{%
+ \refstepcounter{#1}%
+ \@ifnextchar[{\@ydefthm{#1}{#2}}{\@xdefthm{#1}{#2}}%
+}
+\def\@xdefthm#1#2{%
+ \@begindef{#2}{\csname the#1\endcsname}%
+ \ignorespaces
+}
+\def\@ydefthm#1#2[#3]{%
+ \trivlist
+ \item[%
+ \hskip 10\p@
+ \hskip \labelsep
+ {\it #2%
+ \savebox\@tempboxa{#3}%
+ \ifdim \wd\@tempboxa>\z@
+ \ \box\@tempboxa
+ \fi.%
+ }]%
+ \ignorespaces
+}
+\def\@begindef#1#2{%
+ \trivlist
+ \item[%
+ \hskip 10\p@
+ \hskip \labelsep
+ {\it #1\ \rm #2.}%
+ ]%
+}
+\def\theequation{\arabic{equation}}
+
+\newcounter{part}
+\newcounter{section}
+\newcounter{subsection}[section]
+\newcounter{subsubsection}[subsection]
+\newcounter{paragraph}[subsubsection]
+\def\thepart{\Roman{part}}
+\def\thesection{\arabic{section}}
+\def\thesubsection{\thesection.\arabic{subsection}}
+\def\thesubsubsection{\thesubsection.\arabic{subsubsection}} %removed \subsecfnt 29 July 2002 gkmt
+\def\theparagraph{\thesubsubsection.\arabic{paragraph}} %removed \subsecfnt 29 July 2002 gkmt
+
+\newif\if at uchead
+\@ucheadfalse
+
+%% CHANGES: NEW NOTE
+%% NOTE: OK to use old-style font commands below, since they were
+%% suitably redefined for LaTeX2e
+%% END CHANGES
+\setcounter{secnumdepth}{3}
+\def\part{%
+ \@startsection{part}{9}{\z@}{-10\p@ \@plus -4\p@ \@minus -2\p@}
+ {4\p@}{\normalsize\@ucheadtrue}%
+}
+
+% Rationale for changes made in next four definitions:
+% "Before skip" is made elastic to provide some give in setting columns (vs.
+% parskip, which is non-elastic to keep section headers "anchored" to their
+% subsequent text.
+%
+% "After skip" is minimized -- BUT setting it to 0pt resulted in run-in heads, despite
+% the documentation asserted only after-skip < 0pt would have result.
+%
+% Baselineskip added to style to ensure multi-line section titles, and section heads
+% followed by another section head rather than text, are decently spaced vertically.
+% 12 Jan 2000 gkmt
+\def\section{%
+ \@startsection{section}{1}{\z@}{-10\p@ \@plus -4\p@ \@minus -2\p@}%
+ {0.5pt}{\baselineskip=14pt\secfnt\@ucheadtrue}%
+}
+
+\def\subsection{%
+ \@startsection{subsection}{2}{\z@}{-10\p@ \@plus -4\p@ \@minus -2\p@}
+ {0.5pt}{\baselineskip=14pt\secfnt}%
+}
+\def\subsubsection{%
+ \@startsection{subsubsection}{3}{\z@}{-10\p@ \@plus -4\p@ \@minus -2\p@}%
+ {0.5pt}{\baselineskip=14pt\subsecfnt}%
+}
+
+\def\paragraph{%
+ \@startsection{paragraph}{3}{\z@}{-10\p@ \@plus -4\p@ \@minus -2\p@}%
+ {0.5pt}{\baselineskip=14pt\subsecfnt}%
+}
+
+\let\@period=.
+\def\@startsection#1#2#3#4#5#6{%
+ \if at noskipsec %gkmt, 11 aug 99
+ \global\let\@period\@empty
+ \leavevmode
+ \global\let\@period.%
+ \fi
+ \par
+ \@tempskipa #4\relax
+ \@afterindenttrue
+ \ifdim \@tempskipa <\z@
+ \@tempskipa -\@tempskipa
+ \@afterindentfalse
+ \fi
+ %\if at nobreak 11 Jan 00 gkmt
+ %\everypar{}
+ %\else
+ \addpenalty\@secpenalty
+ \addvspace\@tempskipa
+ %\fi
+ \parskip=0pt
+ \@ifstar
+ {\@ssect{#3}{#4}{#5}{#6}}
+ {\@dblarg{\@sect{#1}{#2}{#3}{#4}{#5}{#6}}}%
+}
+
+
+\def\@ssect#1#2#3#4#5{%
+ \@tempskipa #3\relax
+ \ifdim \@tempskipa>\z@
+ \begingroup
+ #4{%
+ \@hangfrom{\hskip #1}%
+ \interlinepenalty \@M #5\@@par}%
+ \endgroup
+ \else
+ \def\@svsechd{#4{\hskip #1\relax #5}}%
+ \fi
+ \vskip -10.5pt %gkmt, 7 jan 00 -- had been -14pt, now set to parskip
+ \@xsect{#3}\parskip=10.5pt} % within the starred section, parskip = leading 12 Jan 2000 gkmt
+
+
+\def\@sect#1#2#3#4#5#6[#7]#8{%
+ \ifnum #2>\c at secnumdepth
+ \let\@svsec\@empty
+ \else
+ \refstepcounter{#1}%
+ \edef\@svsec{%
+ \begingroup
+ %\ifnum#2>2 \noexpand\rm \fi % changed to next 29 July 2002 gkmt
+ \ifnum#2>2 \noexpand#6 \fi
+ \csname the#1\endcsname
+ \endgroup
+ \ifnum #2=1\relax .\fi
+ \hskip 1em
+ }%
+ \fi
+ \@tempskipa #5\relax
+ \ifdim \@tempskipa>\z@
+ \begingroup
+ #6\relax
+ \@hangfrom{\hskip #3\relax\@svsec}%
+ \begingroup
+ \interlinepenalty \@M
+ \if at uchead
+ \uppercase{#8}%
+ \else
+ #8%
+ \fi
+ \par
+ \endgroup
+ \endgroup
+ \csname #1mark\endcsname{#7}%
+ \vskip -10.5pt % -14pt gkmt, 11 aug 99 -- changed to -\parskip 11 Jan 2000
+ \addcontentsline{toc}{#1}{%
+ \ifnum #2>\c at secnumdepth \else
+ \protect\numberline{\csname the#1\endcsname}%
+ \fi
+ #7%
+ }%
+ \else
+ \def\@svsechd{%
+ #6%
+ \hskip #3\relax
+ \@svsec
+ \if at uchead
+ \uppercase{#8}%
+ \else
+ #8%
+ \fi
+ \csname #1mark\endcsname{#7}%
+ \addcontentsline{toc}{#1}{%
+ \ifnum #2>\c at secnumdepth \else
+ \protect\numberline{\csname the#1\endcsname}%
+ \fi
+ #7%
+ }%
+ }%
+ \fi
+ \@xsect{#5}\parskip=10.5pt% within the section, parskip = leading 12 Jan 2000 gkmt
+}
+\def\@xsect#1{%
+ \@tempskipa #1\relax
+ \ifdim \@tempskipa>\z@
+ \par
+ \nobreak
+ \vskip \@tempskipa
+ \@afterheading
+ \else
+ \global\@nobreakfalse
+ \global\@noskipsectrue
+ \everypar{%
+ \if at noskipsec
+ \global\@noskipsecfalse
+ \clubpenalty\@M
+ \hskip -\parindent
+ \begingroup
+ \@svsechd
+ \@period
+ \endgroup
+ \unskip
+ \@tempskipa #1\relax
+ \hskip -\@tempskipa
+ \else
+ \clubpenalty \@clubpenalty
+ \everypar{}%
+ \fi
+ }%
+ \fi
+ \ignorespaces
+}
+
+\def\@trivlist{%
+ \@topsepadd\topsep
+ \if at noskipsec
+ \global\let\@period\@empty
+ \leavevmode
+ \global\let\@period.%
+ \fi
+ \ifvmode
+ \advance\@topsepadd\partopsep
+ \else
+ \unskip
+ \par
+ \fi
+ \if at inlabel
+ \@noparitemtrue
+ \@noparlisttrue
+ \else
+ \@noparlistfalse
+ \@topsep\@topsepadd
+ \fi
+ \advance\@topsep \parskip
+ \leftskip\z at skip
+ \rightskip\@rightskip
+ \parfillskip\@flushglue
+ \@setpar{\if at newlist\else{\@@par}\fi}
+ \global\@newlisttrue
+ \@outerparskip\parskip
+}
+
+%%% Actually, 'abbrev' works just fine as the default - Gerry Feb. 2000
+%%% Bibliography style.
+
+\parindent 0pt
+\typeout{Using 'Abbrev' bibliography style}
+\newcommand\bibyear[2]{%
+ \unskip\quad\ignorespaces#1\unskip
+ \if#2..\quad \else \quad#2 \fi
+}
+\newcommand{\bibemph}[1]{{\em#1}}
+\newcommand{\bibemphic}[1]{{\em#1\/}}
+\newcommand{\bibsc}[1]{{\sc#1}}
+\def\@normalcite{%
+ \def\@cite##1##2{[##1\if at tempswa , ##2\fi]}%
+}
+\def\@citeNB{%
+ \def\@cite##1##2{##1\if at tempswa , ##2\fi}%
+}
+\def\@citeRB{%
+ \def\@cite##1##2{##1\if at tempswa , ##2\fi]}%
+}
+\def\start at cite#1#2{%
+ \edef\citeauthoryear##1##2##3{%
+ ###1%
+ \ifnum#2=\z@ \else\ ###2\fi
+ }%
+ \ifnum#1=\thr@@
+ \let\@@cite\@citeyear
+ \else
+ \let\@@cite\@citenormal
+ \fi
+ \@ifstar{\@citeNB\@@cite}{\@normalcite\@@cite}%
+}
+\def\cite{\start at cite23}
+\def\citeNP{\cite*}
+\def\citeA{\start at cite10}
+\def\citeANP{\citeA*}
+\def\shortcite{\start at cite23}
+\def\shortciteNP{\shortcite*}
+\def\shortciteA{\start at cite20}
+\def\shortciteANP{\shortciteA*}
+\def\citeyear{\start at cite30}
+\def\citeyearNP{\citeyear*}
+\def\citeN{%
+ \@citeRB
+ \def\citeauthoryear##1##2##3{##1\ [##3%
+ \def\reserved at a{##1}%
+ \def\citeauthoryear####1####2####3{%
+ \def\reserved at b{####1}%
+ \ifx\reserved at a\reserved at b
+ ####3%
+ \else
+ \errmessage{Package acmart Error: author mismatch
+ in \string\citeN^^J^^J%
+ See the acmart package documentation for explanation}%
+ \fi
+ }%
+ }%
+ \@ifstar\@citeyear\@citeyear
+}
+\def\shortciteN{%
+ \@citeRB
+ \def\citeauthoryear##1##2##3{##2\ [##3%
+ \def\reserved at a{##2}%
+ \def\citeauthoryear####1####2####3{%
+ \def\reserved at b{####2}%
+ \ifx\reserved at a\reserved at b
+ ####3%
+ \else
+ \errmessage{Package acmart Error: author mismatch
+ in \string\shortciteN^^J^^J%
+ See the acmart package documentation for explanation}%
+ \fi
+ }%
+ }%
+ \@ifstar\@citeyear\@citeyear % changed from "\@ifstart" 12 Jan 2000 gkmt
+}
+
+\def\@citenormal{%
+ \@ifnextchar [{\@tempswatrue\@citex;}
+ {\@tempswafalse\@citex,[]}% was ; Gerry 2/24/00
+}
+\def\@citeyear{%
+ \@ifnextchar [{\@tempswatrue\@citex,}%
+ {\@tempswafalse\@citex,[]}%
+}
+\def\@citex#1[#2]#3{%
+ \let\@citea\@empty
+ \@cite{%
+ \@for\@citeb:=#3\do{%
+ \@citea
+ \def\@citea{#1 }%
+ \edef\@citeb{\expandafter\@iden\@citeb}%
+ \if at filesw
+ \immediate\write\@auxout{\string\citation{\@citeb}}%
+ \fi
+ \@ifundefined{b@\@citeb}{%
+ {\bf ?}%
+ \@warning{%
+ Citation `\@citeb' on page \thepage\space undefined%
+ }%
+ }%
+ {\csname b@\@citeb\endcsname}%
+ }%
+ }{#2}%
+}
+\let\@biblabel\@gobble
+\newdimen\bibindent
+\setcounter{enumi}{1}
+\bibindent=0em
+\def\thebibliography#1{%
+\ifnum\addauflag=0\addauthorsection\global\addauflag=1\fi
+ \section{%
+ {References} % was uppercased but this affects pdf bookmarks (SP/GM Oct. 2004)
+ \@mkboth{{\refname}}{{\refname}}%
+ }%
+ \list{[\arabic{enumi}]}{%
+ \settowidth\labelwidth{[#1]}%
+ \leftmargin\labelwidth
+ \advance\leftmargin\labelsep
+ \advance\leftmargin\bibindent
+ \itemindent -\bibindent
+ \listparindent \itemindent
+ \usecounter{enumi}
+ }%
+ \let\newblock\@empty
+ \raggedright %% 7 JAN 2000 gkmt
+ \sloppy
+ \sfcode`\.=1000\relax
+}
+
+
+\gdef\balancecolumns
+{\vfill\eject
+\global\@colht=\textheight
+\global\ht\@cclv=\textheight
+}
+
+\newcount\colcntr
+\global\colcntr=0
+\newbox\savebox
+
+\gdef \@makecol {%
+\global\advance\colcntr by 1
+\ifnum\colcntr>2 \global\colcntr=1\fi
+ \ifvoid\footins
+ \setbox\@outputbox \box\@cclv
+ \else
+ \setbox\@outputbox \vbox{%
+\boxmaxdepth \@maxdepth
+ \@tempdima\dp\@cclv
+ \unvbox \@cclv
+ \vskip-\@tempdima
+ \vskip \skip\footins
+ \color at begingroup
+ \normalcolor
+ \footnoterule
+ \unvbox \footins
+ \color at endgroup
+ }%
+ \fi
+ \xdef\@freelist{\@freelist\@midlist}%
+ \global \let \@midlist \@empty
+ \@combinefloats
+ \ifvbox\@kludgeins
+ \@makespecialcolbox
+ \else
+ \setbox\@outputbox \vbox to\@colht {%
+\@texttop
+ \dimen@ \dp\@outputbox
+ \unvbox \@outputbox
+ \vskip -\dimen@
+ \@textbottom
+ }%
+ \fi
+ \global \maxdepth \@maxdepth
+}
+\def\titlenote{\@ifnextchar[\@xtitlenote{\stepcounter\@mpfn
+\global\advance\titlenotecount by 1
+\ifnum\titlenotecount=1
+ \raisebox{9pt}{$\ast$}
+\fi
+\ifnum\titlenotecount=2
+ \raisebox{9pt}{$\dagger$}
+\fi
+\ifnum\titlenotecount=3
+ \raisebox{9pt}{$\ddagger$}
+\fi
+\ifnum\titlenotecount=4
+\raisebox{9pt}{$\S$}
+\fi
+\ifnum\titlenotecount=5
+\raisebox{9pt}{$\P$}
+\fi
+ \@titlenotetext
+}}
+
+\long\def\@titlenotetext#1{\insert\footins{%
+\ifnum\titlenotecount=1\global\tntoks={#1}\fi
+\ifnum\titlenotecount=2\global\tntokstwo={#1}\fi
+\ifnum\titlenotecount=3\global\tntoksthree={#1}\fi
+\ifnum\titlenotecount=4\global\tntoksfour={#1}\fi
+\ifnum\titlenotecount=5\global\tntoksfive={#1}\fi
+ \reset at font\footnotesize
+ \interlinepenalty\interfootnotelinepenalty
+ \splittopskip\footnotesep
+ \splitmaxdepth \dp\strutbox \floatingpenalty \@MM
+ \hsize\columnwidth \@parboxrestore
+ \protected at edef\@currentlabel{%
+ }%
+ \color at begingroup
+ \color at endgroup}}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%
+\ps at plain
+\baselineskip=11pt
+\let\thepage\relax % For NO page numbers - Gerry Nov. 30th. 1999
+\def\setpagenumber#1{\global\setcounter{page}{#1}}
+%\pagenumbering{arabic} % Arabic page numbers but commented out for NO page numbes - Gerry Nov. 30th. 1999
+\twocolumn % Double column.
+\flushbottom % Even bottom -- alas, does not balance columns at end of document
+\pagestyle{plain}
+
+% Need Copyright Year and Copyright Data to be user definable (in .tex file).
+% Gerry Nov. 30th. 1999
+\newtoks\copyrtyr
+\newtoks\acmcopyr
+\newtoks\boilerplate
+\def\CopyrightYear#1{\global\copyrtyr{#1}}
+\def\crdata#1{\global\acmcopyr{#1}}
+\def\permission#1{\global\boilerplate{#1}}
+%
+\newtoks\copyrightetc
+\global\copyrightetc{\ } % Need to have 'something' so that adequate space is left for pasting in a line if "confinfo" is supplied.
+
+\toappear{\the\boilerplate\par
+{\confname{\the\conf}} \the\confinfo\par \the\copyrightetc}
+% End of ACM_PROC_ARTICLE-SP.CLS -- V2.7SP - 10/15/2004 --
+% Gerry Murray -- October 15th. 2004
Added: trunk/community/papers/05_biomed_bio/debian-med-bio-llncs.tex
===================================================================
--- trunk/community/papers/05_biomed_bio/debian-med-bio-llncs.tex (rev 0)
+++ trunk/community/papers/05_biomed_bio/debian-med-bio-llncs.tex 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,121 @@
+% debian-med-bio.tex
+% ACM SIG Proceedings document using LaTeX2e
+% Authors: Andreas Tille, Steffen Möller
+% Revisions: 28 April 2005
+% 03 May 2005
+
+
+%\documentclass{sig-alternate}
+\documentclass{llncs}
+%\usepackage{natbib} %%% COMMENT at: Seems to fix the \babel-cite problem but
+ %%% leads to other errors
+\usepackage{times}
+\newif\ifpdf
+\ifx\pdfoutput\undefined
+ \pdffalse % we do not use PDFLaTeX
+ \PassOptionsToPackage{dvips}{graphics}
+ \PassOptionsToPackage{dvipdfm}{hyperref}
+\else
+ \pdfoutput=1 % we use PDFLaTeX
+ \pdftrue
+ \PassOptionsToPackage{pdftex}{graphics}
+ \PassOptionsToPackage{pdftex}{hyperref}
+\fi
+\usepackage{graphics,color}
+\usepackage[latin1]{inputenc}
+\ifpdf
+ \PassOptionsToPackage{pdftex,colorlinks=true,urlcolor=blue,linkcolor=blue}{hyperref}
+ \pdfcompresslevel=9
+\else
+ \usepackage{url}
+\fi
+
+\usepackage{html}
+%\usepackage{hyperref}
+
+\usepackage[T1]{fontenc}
+%%%%\usepackage[english]{babel} %%% conflicts with \cite !!!
+\usepackage{xspace}
+
+\def\addbibtoc{
+\addcontentsline{toc}{section}{\numberline{\mbox{}}\relax\bibname}
+}
+
+\newcommand{\Path}[1]{\path{#1}\xspace}
+\newcommand{\onlynameurl}[1]{\Path{#1}}
+\newcommand{\package}[1]{\Path{#1}}
+\newcommand{\command}[1]{\Path{#1}}
+\newcommand{\file}[1]{\Path{#1}}
+
+\newcommand{\printemail}[1]{%
+ \ifpdf
+ \href{mailto:#1}{$<$#1$>$}%
+ \else
+ \onlynameurl{$<$#1$>$}%
+ \fi
+ \xspace
+}
+\newcommand{\printurl}[2]{%
+ \htmladdnormallink{#2}{http://#1}%
+% \href{http://#1}{#2}%
+% \ifpdf
+% \htmladdnormallink{#2}{http://#1}%
+% \else
+% \onlynameurl{#2}%
+% \fi
+ \xspace
+}
+
+\newcommand{\myinsertgraphic}[1]{%
+ \ifpdf
+ % \resizebox{#2}{#3}{%
+ \resizebox{80mm}{53mm}{%
+ \includegraphics{#1}%
+ }%
+ \else
+ \includegraphics{#1}%
+ %%\epsfig{file=#1.eps}%, height=#2, width=#3}
+ \fi
+}
+
+\def\halfsloppy{%
+ \tolerance 1250%
+ \emergencystretch 0.75em}
+
+\date{28 April 2005}
+
+\begin{document}
+%\mainmatter
+\title{Free Software In Biology Using Debian-Med: A Resource For Information Agents and Computational Grids}
+
+\titlerunning{Debian-Med}
+\institute{Robert Koch-Institut,
+ Burgstr. 37,
+ 38855 Wernigerode,
+ Germany, \\
+ \email{tillea at rki.de}, \\
+ \printurl{fam-tille.de}{\texttt{http://fam-tille.de}}
+\and
+ University of Rostock,
+ Institute of Immunology,
+ Schillingallee 70,
+ 18059 Rostock,
+ Germany, \\
+ \email{moeller at pzr.uni-rostock.de}, \\
+ \printurl{bioinformatics.pzr.uni-rostock.de}{\texttt{http://bioinformatics.pzr.uni-rostock.de}}
+}
+
+%% \and leads to errors
+%% \author{Andreas Tille \and Steffen Möller}
+%% Just use simple "and"
+\author{Andreas Tille\inst{1} and Steffen Möller\inst{2}}
+
+\maketitle
+
+\input paper-text
+
+\bibliographystyle{is-unsrt}
+%%\bibliographystyle{splncs}
+\bibliography{debian-med-bio}
+
+\end{document}
Added: trunk/community/papers/05_biomed_bio/debian-med-bio.bib
===================================================================
--- trunk/community/papers/05_biomed_bio/debian-med-bio.bib (rev 0)
+++ trunk/community/papers/05_biomed_bio/debian-med-bio.bib 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,250 @@
+ at ARTICLE{bar:openmosix,
+ AUTHOR = "M. Bar and B. Knox",
+ TITLE = {{OpenMosix: The Other Kind of HPC Cluster}},
+ JOURNAL = "ClusterWorld",
+ VOLUME = {2},
+ NUMBER = {12},
+ YEAR = {2004},
+ URL = {http://www.openmosix.org}
+ }
+
+ at ARTICLE{eddelbuettel:quantian,
+ AUTHOR = "Dirk Eddelbuettel",
+ TITLE = {{Quantian: A Scientific Computing Environment}},
+ JOURNAL = {Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003)},
+ VOLUME = {12},
+ NUMBER = {2},
+ PAGES = {291-301},
+ MONTH = "March",
+ YEAR = {2003},
+ URL = {http://dirk.eddelbuettel.com/quantian},
+ note = {Vienna, Austria},
+ editors = "Hornik K., Leisch F., Zeileis A."
+ }
+
+ at ARTICLE{dfsg,
+ AUTHOR = "Bruce Perens and Ean Schuessler and Debian",
+ TITLE = {{Debian Free Software Guidelines}},
+ ORGANIZATION = "Debian",
+ MONTH = "June",
+ YEAR = {1997},
+ URL = {http://www.debian.org/social_contract#guidelines}
+ }
+
+ at INPROCEEDINGS{tille:ltk03,
+ AUTHOR = "Andreas Tille",
+ TITLE = {{Freie Software im Gesundheitswesen}},
+ BOOKTITLE = "Proceedings LinuxTag 2003",
+ ORGANIZATION = "LinuxTag",
+ MONTH = "July",
+ YEAR = {2003},
+ URL = {http://people.debian.org/%7Etille/talks/200307_ltk/paper-305-de.html}
+ }
+
+ at ARTICLE{tille:cdd,
+ AUTHOR = "Andreas Tille",
+ TITLE = {{Custom Debian Distributions}},
+ ORGANIZATION = "Debian",
+ MONTH = "June",
+ YEAR = {2004},
+ URL = {http://people.debian.org/%7Etille/cdd}
+ }
+
+ at INPROCEEDINGS{eerola:2004,
+ AUTHOR = "P. Eerola and T. Ekelöf and M. Ellert and J.R. Hansen and A. Konstantinov and B. Konya and J.L. Nielsen and F. Ould-Saada and O. Smirnova and A. Wäänänen",
+ TITLE = {{Science on NorduGrid}},
+ BOOKTITLE = "ECCOMAS 2004",
+ YEAR = "2004",
+ URL = {http://www.nordugrid.org/documents/eccomas04.pdf}
+ }
+
+ at ARTICLE{foster:2001,
+ AUTHOR="Foster I., Kesselman C., Tuecke S.",
+ YEAR=2001,
+ TITLE={{The Anatomy of the Grid: Enabling Scalable Virtual Organizations.}},
+ JOURNAL="International J. Supercomputer Applications",
+ VOLUME=15,
+ NUMBER=3
+}
+
+ at ARTICLE{hubbard:2005,
+ AUTHOR="T. Hubbard and D. Andrews and M. Caccamo and G. Cameron and Y. Chen and M. Clamp and L. Clarke and G. Coates and T. Cox and F. Cunningham and V. Curwen and T. Cutts and T. Down and R. Durbin and X.M. Fernandez-Suarez and J. Gilbert and M. Hammond and J. Herrero and H. Hotz and K. Howe and V. Iyer and K. Jekosch and A. Kahari and A. Kasprzyk and D. Keefe and S. Keenan and F. Kokocinsci and D. London and I. Longden and G. McVicker and C. Melsopp and P. Meidl and S. Potter and G. Proctor and M. Rae and D. Rios and M. Schuster and S. Searle and J. Severin and G. Slater and D. Smedley and J. Smith and W. Spooner and A. Stabenau and J. Stalker and R. Storey and S. Trevanion and A. Ureta-Vidal and J. Vogel and S. White and C. Woodwark and E. Birney",
+ TITLE="Ensembl 2005.",
+ JOURNAL="Nucleic Acids Res.",
+ YEAR=2005,
+ VOLUME=33,
+ NUMBER=1,
+ PAGES="D447-D453"
+}
+ at ARTICLE{stevens:2004,
+ AUTHOR="R. Stevens and H.J. Tipney and C. Wroe and T. Oinn and M. Senger and P. Lord and C.A. Goble C.A. and A. Brass and M. Tassabehji",
+ TITLE={{Exploring Williams-Beuren Syndrome Using myGrid}},
+ YEAR=2004,
+ ADDRESS="Glasgow, UK",
+ JOURNAL="Bioinformatics",
+ VOLUME=20,
+ NUMBER="Suppl. 1",
+ PAGES="i303-i310",
+ URL="http://www.mygrid.org.uk"
+}
+ at article{wilkinson:2005,
+ AUTHOR="M. Wilkinson and H. Schoof and R. Ernst and D. Haase",
+ YEAR=2005,
+ TITLE={{BioMOBY successfully integrates disributed heterogenous bioinformatics web services. The PlaNet exemplar case.}},
+ JOURNAL="Plant Physol.",
+ VOLUME=138,
+ PAGES="1-13"
+}
+ at ARTICLE{zdobnow:2002,
+ AUTHOR="E.M. Zdobnov and R. Lopez and R. Apweiler and T. Etzold",
+ TITLE={{The EBI SRS server-new features}},
+ JOURNAL="Bioinformatics",
+ YEAR=2002,
+ VOLUME=18,
+ NUMBER=8,
+ PAGES="1149-1150",
+ URL="http://srs.ebi.ac.uk"
+}
+ at INPROCEEDINGS{lord:2004,
+ AUTHOR="P. Lord and S. Bechhofer and M.D. Wilkinson and G. Schiltz and D. Gessler and D. Hull and C. Goble and L. Stein",
+ YEAR=2004,
+ TITLE={{Applying semantic web services to Bioinformatics: Experiences gained, lessons learnt}},
+ BOOKTITLE="ISWC",
+ PUBLISHER="Springer-Verlag Berlin Heidelberg",
+ PAGES="350-364"
+}
+
+ at INPROCEEDINGS{merelli:2002,
+ AUTHOR="E. Merelli and L. Culmone and L. Mariani",
+ TITLE={{BioAgent: A Mobile Agent System for Bioscientists}},
+ BOOKTITLE="NETTAB02 Agents in Bioinformatics, Bologna",
+ YEAR="2002",
+ URL="http://www.bioagent.net"
+}
+
+ at ARTICLE{fink:2005,
+ AUTHOR="Fink Development Team",
+ TITLE="Fink",
+ YEAR="2005",
+ URL="http://fink.sourceforge.net"
+}
+
+ at ARTICLE{hess:2003,
+ AUTHOR="Joe Hess",
+ TITLE={{Comparing Linux/UNIX Binary Package Formats}},
+ YEAR="2003",
+ URL="http://www.kitenet.net/%7Ejoey/pkg-comp"
+}
+
+ at ARTICLE{knopper:2005,
+ AUTHOR="Klaus Knopper",
+ TITLE={{Knoppix Live CD}},
+ YEAR="2005",
+ URL="http://www.knopper.net"
+}
+
+ at ARTICLE{kojima:2000,
+ AUTHOR="Alfredo K. Kojima",
+ TITLE={{An RPM port of APT}},
+ YEAR="2000",
+ URL="http://freshmeat.net/articles/view/192 , http://apt4rpm.sourceforge.net"
+}
+
+ at ARTICLE{larsen:2005,
+ AUTHOR="Niels E. Larsen",
+ TITLE={{ARC Knoppix}},
+ YEAR="2005",
+ URL="http://cvs.nordugrid.org/knx/arcknoppix.iso"
+}
+
+ at ARTICLE{larsenscript:2005,
+ AUTHOR="Niels E. Larsen",
+ TITLE={{Script to add the NorduGrid to the basic Knoppix distribution}},
+ YEAR="2005",
+ URL="http://cvs.nordugrid.org/mkknx"
+}
+
+ at ARTICLE{lsb,
+ AUTHOR="LSB Workgroup",
+ TITLE={{Linux Standard Base}},
+ YEAR="2005",
+ URL="http://www.linuxbase.org"
+}
+
+ at ARTICLE{mysql,
+ AUTHOR="MySQL",
+ YEAR="2005",
+ URL="http://www.mysql.com"
+}
+
+
+ at ARTICLE{debianpolicy,
+ AUTHOR="Ian Jackson and Christian Schwarz and Debian",
+ TITLE={{Debian Policy Manual}},
+ YEAR="2005",
+ URL="http://www.debian.org/doc/debian-policy"
+}
+
+
+ at ARTICLE{vandersmissen:2005,
+ AUTHOR="W. Vandersmissen",
+ TITLE="Clusterknoppix",
+ YEAR="2005",
+ URL="http://bofh.be/clusterknoppix"
+}
+
+ at ARTICLE{myers:2003,
+ AUTHOR="Daniel S. Myers and Michael P. Cummings",
+ TITLE={{Necessity is the mother of invention: a simple grid computing system using commodity tools}},
+ JOURNAL="Journal of Parallel and Distributed Computing",
+ Volume=63,
+ NUMBER=5,
+ YEAR=2003,
+ Pages="578-589",
+ URL="http://lattice.umiacs.umd.edu"
+}
+
+ at INPROCEEDINGS{anderson:2004,
+ AUTHOR="David P. Anderson",
+ TITLE={{BOINC: A System for Public-Resource Computing and Storage}},
+ BOOKTITLE="5th IEEE/ACM International Workshop on Grid Computing",
+ YEAR=2004,
+ ADDRESS="Pittsburgh, USA",
+ URL="http://boinc.berkeley.edu"
+}
+
+ at article{Wheeler2005,
+ author="DL Wheeler and T. Barrett and DA Benson and SH Bryant and K. Canese and DM Church and M. DiCuccio and R. Edgar and S. Federhen and W. Helmberg and DL Kenton and O. Khovayko and DJ. Lipman and TL Madden and DR Maglott and J. Ostell and JU Pontius and KD Pruitt and GD Schuler and LM Schriml and E. Sequeira and ST Sherry and K. Sirotkin and G. Starchenko and TO Suzek and R. Tatusov and TA Tatusova and L. Wagner and E. Yaschenko",
+ title={{Database resources of the National Center for Biotechnology Information}},
+ journal="Nucleic Acids Res.",
+ year=2005,
+ volume=33,
+ number="1 (Database issue)",
+ Pages="D39-D45"
+}
+
+ at article{Jenuth2000,
+ author="JP. Jenuth",
+ title={{The NCBI. Publicly available tools and resources on the Web}},
+ journal="Methods Mol. Biol.",
+ year=2000,
+ volume=132,
+ pages="301-312"
+}
+
+ at article{ncbi:2004,
+ author="NCBI",
+ title={{The NCBI C++ Toolkit book}},
+ year=2004,
+ URL="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.chapter.ch_datamod"
+}
+
+ at article{Bellifemine2001,
+ title={{Developing multi-agent systems with a FIPA-compliant agent framework}},
+ author="Fabio Bellifemine and Agostino Poggi and Giovanni Rimassa",
+ booktitle="Software - Practice And Experience",
+ year=2001,
+ volume=31,
+ pages="103-128"
+}
+
Added: trunk/community/papers/05_biomed_bio/debian-med-bio.tex
===================================================================
--- trunk/community/papers/05_biomed_bio/debian-med-bio.tex (rev 0)
+++ trunk/community/papers/05_biomed_bio/debian-med-bio.tex 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,123 @@
+% debian-med-bio.tex
+% ACM SIG Proceedings document using LaTeX2e
+% Authors: Andreas Tille, Steffen Möller
+% Revisions: 28 April 2005
+% 03 May 2005
+
+
+%\documentclass{sig-alternate}
+\documentclass{acm_proc_article-sp}
+%\usepackage{natbib} %%% COMMENT at: Seems to fix the \babel-cite problem but
+ %%% leads to other errors
+\usepackage{times}
+\newif\ifmypdf
+\ifx\pdfoutput\undefined
+ \mypdffalse % we do not use PDFLaTeX
+ \PassOptionsToPackage{dvips}{graphics}
+\else
+ \pdfoutput=1 % we use PDFLaTeX
+ \mypdftrue
+ \PassOptionsToPackage{pdftex}{graphics}
+\fi
+\usepackage{graphics,color}
+\usepackage[latin1]{inputenc}
+\ifmypdf
+ \PassOptionsToPackage{pdftex,colorlinks=true,urlcolor=blue,linkcolor=blue}{hyperref}
+ \pdfcompresslevel=9
+\else
+ \usepackage{url}
+\fi
+\usepackage{html}
+\usepackage[T1]{fontenc}
+%\usepackage[english]{babel} %%% conflicts with \cite !!!
+\usepackage{xspace}
+
+\def\addbibtoc{
+\addcontentsline{toc}{section}{\numberline{\mbox{}}\relax\bibname}
+}
+
+\newcommand{\Path}[1]{\path{#1}\xspace}
+\newcommand{\onlynameurl}[1]{\Path{#1}}
+\newcommand{\package}[1]{\Path{#1}}
+\newcommand{\command}[1]{\Path{#1}}
+\newcommand{\file}[1]{\Path{#1}}
+
+\newcommand{\printemail}[1]{%
+ \ifmypdf
+ \href{mailto:#1}{$<$#1$>$}%
+ \else
+ \onlynameurl{$<$#1$>$}%
+ \fi
+ \xspace
+}
+\newcommand{\printurl}[2]{%
+ \htmladdnormallink{#2}{http://#1}%
+% \ifmypdf
+% \htmladdnormallink{#2}{http://#1}%
+% \else
+% \onlynameurl{#2}%
+% \fi
+ \xspace
+}
+
+\newcommand{\myinsertgraphic}[1]{%
+ \ifmypdf
+ % \resizebox{#2}{#3}{%
+ %\resizebox{80mm}{53mm}{%
+ \includegraphics[width=\textwidth]{#1}%
+ %}%
+ \else
+ \includegraphics{#1}%
+ %%\epsfig{file=#1.eps}%, height=#2, width=#3}
+ \fi
+}
+
+\def\halfsloppy{%
+ \tolerance 1250%
+ \emergencystretch 0.75em}
+
+\date{28 April 2005}
+
+\begin{document}
+%
+% --- Author Metadata here ---
+\conferenceinfo{Multi-Agent Systems for Medicine, Computational
+ Biology, and Bioinformatics}{MAS BIOMED'05, Utrecht, The Netherlands}
+\CopyrightYear{2005}
+%\crdata{0-12345-67-8/90/01} % Allows default copyright data (0-89791-88-6/97/05) to be over-ridden - IF NEED BE.
+% --- End of Author Metadata ---
+\title{Free Software In Biology Using Debian-Med: A Resource For Information Agents and Computational Grids
+\titlenote{This paper is available at \printurl{people.debian.org/\%7Etille/talks}{the authors talk page}}
+}
+%\subtitle{[Extended Abstract]
+%%% Bug in style: \titlenote creates extra page :-(
+\numberofauthors{2}%
+\author{
+\alignauthor Andreas Tille%
+ %\titlenote{Andreas Tille just started the
+ %paper. There is no other reason to name him first}
+\\
+ \affaddr{Robert Koch-Institut}\\
+ \affaddr{Burgstr. 37}\\
+ \affaddr{38855 Wernigerode}\\
+ \affaddr{Germany}\\
+ \email{tillea at rki.de}
+\alignauthor Steffen Möller%
+ %\titlenote{Steffen Möller drastically
+ %enhanced this paper}
+\\
+ \affaddr{University of Rostock}\\
+ \affaddr{Institute of Immunology}\\
+ \affaddr{Schillingallee 70}\\
+ \affaddr{18059 Rostock}\\
+ \affaddr{Germany}\\
+ \email{moeller at pzr.uni-rostock.de}
+}
+\maketitle
+
+\input paper-text
+
+\bibliographystyle{is-abbrv}
+\bibliography{debian-med-bio}
+
+\end{document}
Added: trunk/community/papers/05_biomed_bio/earthkeyring.png
===================================================================
(Binary files differ)
Property changes on: trunk/community/papers/05_biomed_bio/earthkeyring.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/community/papers/05_biomed_bio/llncs.cls
===================================================================
--- trunk/community/papers/05_biomed_bio/llncs.cls (rev 0)
+++ trunk/community/papers/05_biomed_bio/llncs.cls 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,1189 @@
+% LLNCS DOCUMENT CLASS -- version 2.13 (28-Jan-2002)
+% Springer Verlag LaTeX2e support for Lecture Notes in Computer Science
+%
+%%
+%% \CharacterTable
+%% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
+%% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
+%% Digits \0\1\2\3\4\5\6\7\8\9
+%% Exclamation \! Double quote \" Hash (number) \#
+%% Dollar \$ Percent \% Ampersand \&
+%% Acute accent \' Left paren \( Right paren \)
+%% Asterisk \* Plus \+ Comma \,
+%% Minus \- Point \. Solidus \/
+%% Colon \: Semicolon \; Less than \<
+%% Equals \= Greater than \> Question mark \?
+%% Commercial at \@ Left bracket \[ Backslash \\
+%% Right bracket \] Circumflex \^ Underscore \_
+%% Grave accent \` Left brace \{ Vertical bar \|
+%% Right brace \} Tilde \~}
+%%
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\ProvidesClass{llncs}[2002/01/28 v2.13
+^^J LaTeX document class for Lecture Notes in Computer Science]
+% Options
+\let\if at envcntreset\iffalse
+\DeclareOption{envcountreset}{\let\if at envcntreset\iftrue}
+\DeclareOption{citeauthoryear}{\let\citeauthoryear=Y}
+\DeclareOption{oribibl}{\let\oribibl=Y}
+\let\if at custvec\iftrue
+\DeclareOption{orivec}{\let\if at custvec\iffalse}
+\let\if at envcntsame\iffalse
+\DeclareOption{envcountsame}{\let\if at envcntsame\iftrue}
+\let\if at envcntsect\iffalse
+\DeclareOption{envcountsect}{\let\if at envcntsect\iftrue}
+\let\if at runhead\iffalse
+\DeclareOption{runningheads}{\let\if at runhead\iftrue}
+
+\let\if at openbib\iffalse
+\DeclareOption{openbib}{\let\if at openbib\iftrue}
+
+% languages
+\let\switcht@@therlang\relax
+\def\ds at deutsch{\def\switcht@@therlang{\switcht at deutsch}}
+\def\ds at francais{\def\switcht@@therlang{\switcht at francais}}
+
+\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
+
+\ProcessOptions
+
+\LoadClass[twoside]{article}
+\RequirePackage{multicol} % needed for the list of participants, index
+
+\setlength{\textwidth}{12.2cm}
+\setlength{\textheight}{19.3cm}
+\renewcommand\@pnumwidth{2em}
+\renewcommand\@tocrmarg{3.5em}
+%
+\def\@dottedtocline#1#2#3#4#5{%
+ \ifnum #1>\c at tocdepth \else
+ \vskip \z@ \@plus.2\p@
+ {\leftskip #2\relax \rightskip \@tocrmarg \advance\rightskip by 0pt plus 2cm
+ \parfillskip -\rightskip \pretolerance=10000
+ \parindent #2\relax\@afterindenttrue
+ \interlinepenalty\@M
+ \leavevmode
+ \@tempdima #3\relax
+ \advance\leftskip \@tempdima \null\nobreak\hskip -\leftskip
+ {#4}\nobreak
+ \leaders\hbox{$\m at th
+ \mkern \@dotsep mu\hbox{.}\mkern \@dotsep
+ mu$}\hfill
+ \nobreak
+ \hb at xt@\@pnumwidth{\hfil\normalfont \normalcolor #5}%
+ \par}%
+ \fi}
+%
+\def\switcht at albion{%
+\def\abstractname{Abstract.}
+\def\ackname{Acknowledgement.}
+\def\andname{and}
+\def\lastandname{\unskip, and}
+\def\appendixname{Appendix}
+\def\chaptername{Chapter}
+\def\claimname{Claim}
+\def\conjecturename{Conjecture}
+\def\contentsname{Table of Contents}
+\def\corollaryname{Corollary}
+\def\definitionname{Definition}
+\def\examplename{Example}
+\def\exercisename{Exercise}
+\def\figurename{Fig.}
+\def\keywordname{{\bf Key words:}}
+\def\indexname{Index}
+\def\lemmaname{Lemma}
+\def\contriblistname{List of Contributors}
+\def\listfigurename{List of Figures}
+\def\listtablename{List of Tables}
+\def\mailname{{\it Correspondence to\/}:}
+\def\noteaddname{Note added in proof}
+\def\notename{Note}
+\def\partname{Part}
+\def\problemname{Problem}
+\def\proofname{Proof}
+\def\propertyname{Property}
+\def\propositionname{Proposition}
+\def\questionname{Question}
+\def\remarkname{Remark}
+\def\seename{see}
+\def\solutionname{Solution}
+\def\subclassname{{\it Subject Classifications\/}:}
+\def\tablename{Table}
+\def\theoremname{Theorem}}
+\switcht at albion
+% Names of theorem like environments are already defined
+% but must be translated if another language is chosen
+%
+% French section
+\def\switcht at francais{%\typeout{On parle francais.}%
+ \def\abstractname{R\'esum\'e.}%
+ \def\ackname{Remerciements.}%
+ \def\andname{et}%
+ \def\lastandname{ et}%
+ \def\appendixname{Appendice}
+ \def\chaptername{Chapitre}%
+ \def\claimname{Pr\'etention}%
+ \def\conjecturename{Hypoth\`ese}%
+ \def\contentsname{Table des mati\`eres}%
+ \def\corollaryname{Corollaire}%
+ \def\definitionname{D\'efinition}%
+ \def\examplename{Exemple}%
+ \def\exercisename{Exercice}%
+ \def\figurename{Fig.}%
+ \def\keywordname{{\bf Mots-cl\'e:}}
+ \def\indexname{Index}
+ \def\lemmaname{Lemme}%
+ \def\contriblistname{Liste des contributeurs}
+ \def\listfigurename{Liste des figures}%
+ \def\listtablename{Liste des tables}%
+ \def\mailname{{\it Correspondence to\/}:}
+ \def\noteaddname{Note ajout\'ee \`a l'\'epreuve}%
+ \def\notename{Remarque}%
+ \def\partname{Partie}%
+ \def\problemname{Probl\`eme}%
+ \def\proofname{Preuve}%
+ \def\propertyname{Caract\'eristique}%
+%\def\propositionname{Proposition}%
+ \def\questionname{Question}%
+ \def\remarkname{Remarque}%
+ \def\seename{voir}
+ \def\solutionname{Solution}%
+ \def\subclassname{{\it Subject Classifications\/}:}
+ \def\tablename{Tableau}%
+ \def\theoremname{Th\'eor\`eme}%
+}
+%
+% German section
+\def\switcht at deutsch{%\typeout{Man spricht deutsch.}%
+ \def\abstractname{Zusammenfassung.}%
+ \def\ackname{Danksagung.}%
+ \def\andname{und}%
+ \def\lastandname{ und}%
+ \def\appendixname{Anhang}%
+ \def\chaptername{Kapitel}%
+ \def\claimname{Behauptung}%
+ \def\conjecturename{Hypothese}%
+ \def\contentsname{Inhaltsverzeichnis}%
+ \def\corollaryname{Korollar}%
+%\def\definitionname{Definition}%
+ \def\examplename{Beispiel}%
+ \def\exercisename{\"Ubung}%
+ \def\figurename{Abb.}%
+ \def\keywordname{{\bf Schl\"usselw\"orter:}}
+ \def\indexname{Index}
+%\def\lemmaname{Lemma}%
+ \def\contriblistname{Mitarbeiter}
+ \def\listfigurename{Abbildungsverzeichnis}%
+ \def\listtablename{Tabellenverzeichnis}%
+ \def\mailname{{\it Correspondence to\/}:}
+ \def\noteaddname{Nachtrag}%
+ \def\notename{Anmerkung}%
+ \def\partname{Teil}%
+%\def\problemname{Problem}%
+ \def\proofname{Beweis}%
+ \def\propertyname{Eigenschaft}%
+%\def\propositionname{Proposition}%
+ \def\questionname{Frage}%
+ \def\remarkname{Anmerkung}%
+ \def\seename{siehe}
+ \def\solutionname{L\"osung}%
+ \def\subclassname{{\it Subject Classifications\/}:}
+ \def\tablename{Tabelle}%
+%\def\theoremname{Theorem}%
+}
+
+% Ragged bottom for the actual page
+\def\thisbottomragged{\def\@textbottom{\vskip\z@ plus.0001fil
+\global\let\@textbottom\relax}}
+
+\renewcommand\small{%
+ \@setfontsize\small\@ixpt{11}%
+ \abovedisplayskip 8.5\p@ \@plus3\p@ \@minus4\p@
+ \abovedisplayshortskip \z@ \@plus2\p@
+ \belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
+ \def\@listi{\leftmargin\leftmargini
+ \parsep 0\p@ \@plus1\p@ \@minus\p@
+ \topsep 8\p@ \@plus2\p@ \@minus4\p@
+ \itemsep0\p@}%
+ \belowdisplayskip \abovedisplayskip
+}
+
+\frenchspacing
+\widowpenalty=10000
+\clubpenalty=10000
+
+\setlength\oddsidemargin {63\p@}
+\setlength\evensidemargin {63\p@}
+\setlength\marginparwidth {90\p@}
+
+\setlength\headsep {16\p@}
+
+\setlength\footnotesep{7.7\p@}
+\setlength\textfloatsep{8mm\@plus 2\p@ \@minus 4\p@}
+\setlength\intextsep {8mm\@plus 2\p@ \@minus 2\p@}
+
+\setcounter{secnumdepth}{2}
+
+\newcounter {chapter}
+\renewcommand\thechapter {\@arabic\c at chapter}
+
+\newif\if at mainmatter \@mainmattertrue
+\newcommand\frontmatter{\cleardoublepage
+ \@mainmatterfalse\pagenumbering{Roman}}
+\newcommand\mainmatter{\cleardoublepage
+ \@mainmattertrue\pagenumbering{arabic}}
+\newcommand\backmatter{\if at openright\cleardoublepage\else\clearpage\fi
+ \@mainmatterfalse}
+
+\renewcommand\part{\cleardoublepage
+ \thispagestyle{empty}%
+ \if at twocolumn
+ \onecolumn
+ \@tempswatrue
+ \else
+ \@tempswafalse
+ \fi
+ \null\vfil
+ \secdef\@part\@spart}
+
+\def\@part[#1]#2{%
+ \ifnum \c at secnumdepth >-2\relax
+ \refstepcounter{part}%
+ \addcontentsline{toc}{part}{\thepart\hspace{1em}#1}%
+ \else
+ \addcontentsline{toc}{part}{#1}%
+ \fi
+ \markboth{}{}%
+ {\centering
+ \interlinepenalty \@M
+ \normalfont
+ \ifnum \c at secnumdepth >-2\relax
+ \huge\bfseries \partname~\thepart
+ \par
+ \vskip 20\p@
+ \fi
+ \Huge \bfseries #2\par}%
+ \@endpart}
+\def\@spart#1{%
+ {\centering
+ \interlinepenalty \@M
+ \normalfont
+ \Huge \bfseries #1\par}%
+ \@endpart}
+\def\@endpart{\vfil\newpage
+ \if at twoside
+ \null
+ \thispagestyle{empty}%
+ \newpage
+ \fi
+ \if at tempswa
+ \twocolumn
+ \fi}
+
+\newcommand\chapter{\clearpage
+ \thispagestyle{empty}%
+ \global\@topnum\z@
+ \@afterindentfalse
+ \secdef\@chapter\@schapter}
+\def\@chapter[#1]#2{\ifnum \c at secnumdepth >\m at ne
+ \if at mainmatter
+ \refstepcounter{chapter}%
+ \typeout{\@chapapp\space\thechapter.}%
+ \addcontentsline{toc}{chapter}%
+ {\protect\numberline{\thechapter}#1}%
+ \else
+ \addcontentsline{toc}{chapter}{#1}%
+ \fi
+ \else
+ \addcontentsline{toc}{chapter}{#1}%
+ \fi
+ \chaptermark{#1}%
+ \addtocontents{lof}{\protect\addvspace{10\p@}}%
+ \addtocontents{lot}{\protect\addvspace{10\p@}}%
+ \if at twocolumn
+ \@topnewpage[\@makechapterhead{#2}]%
+ \else
+ \@makechapterhead{#2}%
+ \@afterheading
+ \fi}
+\def\@makechapterhead#1{%
+% \vspace*{50\p@}%
+ {\centering
+ \ifnum \c at secnumdepth >\m at ne
+ \if at mainmatter
+ \large\bfseries \@chapapp{} \thechapter
+ \par\nobreak
+ \vskip 20\p@
+ \fi
+ \fi
+ \interlinepenalty\@M
+ \Large \bfseries #1\par\nobreak
+ \vskip 40\p@
+ }}
+\def\@schapter#1{\if at twocolumn
+ \@topnewpage[\@makeschapterhead{#1}]%
+ \else
+ \@makeschapterhead{#1}%
+ \@afterheading
+ \fi}
+\def\@makeschapterhead#1{%
+% \vspace*{50\p@}%
+ {\centering
+ \normalfont
+ \interlinepenalty\@M
+ \Large \bfseries #1\par\nobreak
+ \vskip 40\p@
+ }}
+
+\renewcommand\section{\@startsection{section}{1}{\z@}%
+ {-18\p@ \@plus -4\p@ \@minus -4\p@}%
+ {12\p@ \@plus 4\p@ \@minus 4\p@}%
+ {\normalfont\large\bfseries\boldmath
+ \rightskip=\z@ \@plus 8em\pretolerance=10000 }}
+\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
+ {-18\p@ \@plus -4\p@ \@minus -4\p@}%
+ {8\p@ \@plus 4\p@ \@minus 4\p@}%
+ {\normalfont\normalsize\bfseries\boldmath
+ \rightskip=\z@ \@plus 8em\pretolerance=10000 }}
+\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
+ {-18\p@ \@plus -4\p@ \@minus -4\p@}%
+ {-0.5em \@plus -0.22em \@minus -0.1em}%
+ {\normalfont\normalsize\bfseries\boldmath}}
+\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
+ {-12\p@ \@plus -4\p@ \@minus -4\p@}%
+ {-0.5em \@plus -0.22em \@minus -0.1em}%
+ {\normalfont\normalsize\itshape}}
+\renewcommand\subparagraph[1]{\typeout{LLNCS warning: You should not use
+ \string\subparagraph\space with this class}\vskip0.5cm
+You should not use \verb|\subparagraph| with this class.\vskip0.5cm}
+
+\DeclareMathSymbol{\Gamma}{\mathalpha}{letters}{"00}
+\DeclareMathSymbol{\Delta}{\mathalpha}{letters}{"01}
+\DeclareMathSymbol{\Theta}{\mathalpha}{letters}{"02}
+\DeclareMathSymbol{\Lambda}{\mathalpha}{letters}{"03}
+\DeclareMathSymbol{\Xi}{\mathalpha}{letters}{"04}
+\DeclareMathSymbol{\Pi}{\mathalpha}{letters}{"05}
+\DeclareMathSymbol{\Sigma}{\mathalpha}{letters}{"06}
+\DeclareMathSymbol{\Upsilon}{\mathalpha}{letters}{"07}
+\DeclareMathSymbol{\Phi}{\mathalpha}{letters}{"08}
+\DeclareMathSymbol{\Psi}{\mathalpha}{letters}{"09}
+\DeclareMathSymbol{\Omega}{\mathalpha}{letters}{"0A}
+
+\let\footnotesize\small
+
+\if at custvec
+\def\vec#1{\mathchoice{\mbox{\boldmath$\displaystyle#1$}}
+{\mbox{\boldmath$\textstyle#1$}}
+{\mbox{\boldmath$\scriptstyle#1$}}
+{\mbox{\boldmath$\scriptscriptstyle#1$}}}
+\fi
+
+\def\squareforqed{\hbox{\rlap{$\sqcap$}$\sqcup$}}
+\def\qed{\ifmmode\squareforqed\else{\unskip\nobreak\hfil
+\penalty50\hskip1em\null\nobreak\hfil\squareforqed
+\parfillskip=0pt\finalhyphendemerits=0\endgraf}\fi}
+
+\def\getsto{\mathrel{\mathchoice {\vcenter{\offinterlineskip
+\halign{\hfil
+$\displaystyle##$\hfil\cr\gets\cr\to\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\textstyle##$\hfil\cr\gets
+\cr\to\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptstyle##$\hfil\cr\gets
+\cr\to\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptscriptstyle##$\hfil\cr
+\gets\cr\to\cr}}}}}
+\def\lid{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil
+$\displaystyle##$\hfil\cr<\cr\noalign{\vskip1.2pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\textstyle##$\hfil\cr<\cr
+\noalign{\vskip1.2pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptstyle##$\hfil\cr<\cr
+\noalign{\vskip1pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptscriptstyle##$\hfil\cr
+<\cr
+\noalign{\vskip0.9pt}=\cr}}}}}
+\def\gid{\mathrel{\mathchoice {\vcenter{\offinterlineskip\halign{\hfil
+$\displaystyle##$\hfil\cr>\cr\noalign{\vskip1.2pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\textstyle##$\hfil\cr>\cr
+\noalign{\vskip1.2pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptstyle##$\hfil\cr>\cr
+\noalign{\vskip1pt}=\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptscriptstyle##$\hfil\cr
+>\cr
+\noalign{\vskip0.9pt}=\cr}}}}}
+\def\grole{\mathrel{\mathchoice {\vcenter{\offinterlineskip
+\halign{\hfil
+$\displaystyle##$\hfil\cr>\cr\noalign{\vskip-1pt}<\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\textstyle##$\hfil\cr
+>\cr\noalign{\vskip-1pt}<\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptstyle##$\hfil\cr
+>\cr\noalign{\vskip-0.8pt}<\cr}}}
+{\vcenter{\offinterlineskip\halign{\hfil$\scriptscriptstyle##$\hfil\cr
+>\cr\noalign{\vskip-0.3pt}<\cr}}}}}
+\def\bbbr{{\rm I\!R}} %reelle Zahlen
+\def\bbbm{{\rm I\!M}}
+\def\bbbn{{\rm I\!N}} %natuerliche Zahlen
+\def\bbbf{{\rm I\!F}}
+\def\bbbh{{\rm I\!H}}
+\def\bbbk{{\rm I\!K}}
+\def\bbbp{{\rm I\!P}}
+\def\bbbone{{\mathchoice {\rm 1\mskip-4mu l} {\rm 1\mskip-4mu l}
+{\rm 1\mskip-4.5mu l} {\rm 1\mskip-5mu l}}}
+\def\bbbc{{\mathchoice {\setbox0=\hbox{$\displaystyle\rm C$}\hbox{\hbox
+to0pt{\kern0.4\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\textstyle\rm C$}\hbox{\hbox
+to0pt{\kern0.4\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptstyle\rm C$}\hbox{\hbox
+to0pt{\kern0.4\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptscriptstyle\rm C$}\hbox{\hbox
+to0pt{\kern0.4\wd0\vrule height0.9\ht0\hss}\box0}}}}
+\def\bbbq{{\mathchoice {\setbox0=\hbox{$\displaystyle\rm
+Q$}\hbox{\raise
+0.15\ht0\hbox to0pt{\kern0.4\wd0\vrule height0.8\ht0\hss}\box0}}
+{\setbox0=\hbox{$\textstyle\rm Q$}\hbox{\raise
+0.15\ht0\hbox to0pt{\kern0.4\wd0\vrule height0.8\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptstyle\rm Q$}\hbox{\raise
+0.15\ht0\hbox to0pt{\kern0.4\wd0\vrule height0.7\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptscriptstyle\rm Q$}\hbox{\raise
+0.15\ht0\hbox to0pt{\kern0.4\wd0\vrule height0.7\ht0\hss}\box0}}}}
+\def\bbbt{{\mathchoice {\setbox0=\hbox{$\displaystyle\rm
+T$}\hbox{\hbox to0pt{\kern0.3\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\textstyle\rm T$}\hbox{\hbox
+to0pt{\kern0.3\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptstyle\rm T$}\hbox{\hbox
+to0pt{\kern0.3\wd0\vrule height0.9\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptscriptstyle\rm T$}\hbox{\hbox
+to0pt{\kern0.3\wd0\vrule height0.9\ht0\hss}\box0}}}}
+\def\bbbs{{\mathchoice
+{\setbox0=\hbox{$\displaystyle \rm S$}\hbox{\raise0.5\ht0\hbox
+to0pt{\kern0.35\wd0\vrule height0.45\ht0\hss}\hbox
+to0pt{\kern0.55\wd0\vrule height0.5\ht0\hss}\box0}}
+{\setbox0=\hbox{$\textstyle \rm S$}\hbox{\raise0.5\ht0\hbox
+to0pt{\kern0.35\wd0\vrule height0.45\ht0\hss}\hbox
+to0pt{\kern0.55\wd0\vrule height0.5\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptstyle \rm S$}\hbox{\raise0.5\ht0\hbox
+to0pt{\kern0.35\wd0\vrule height0.45\ht0\hss}\raise0.05\ht0\hbox
+to0pt{\kern0.5\wd0\vrule height0.45\ht0\hss}\box0}}
+{\setbox0=\hbox{$\scriptscriptstyle\rm S$}\hbox{\raise0.5\ht0\hbox
+to0pt{\kern0.4\wd0\vrule height0.45\ht0\hss}\raise0.05\ht0\hbox
+to0pt{\kern0.55\wd0\vrule height0.45\ht0\hss}\box0}}}}
+\def\bbbz{{\mathchoice {\hbox{$\mathsf\textstyle Z\kern-0.4em Z$}}
+{\hbox{$\mathsf\textstyle Z\kern-0.4em Z$}}
+{\hbox{$\mathsf\scriptstyle Z\kern-0.3em Z$}}
+{\hbox{$\mathsf\scriptscriptstyle Z\kern-0.2em Z$}}}}
+
+\let\ts\,
+
+\setlength\leftmargini {17\p@}
+\setlength\leftmargin {\leftmargini}
+\setlength\leftmarginii {\leftmargini}
+\setlength\leftmarginiii {\leftmargini}
+\setlength\leftmarginiv {\leftmargini}
+\setlength \labelsep {.5em}
+\setlength \labelwidth{\leftmargini}
+\addtolength\labelwidth{-\labelsep}
+
+\def\@listI{\leftmargin\leftmargini
+ \parsep 0\p@ \@plus1\p@ \@minus\p@
+ \topsep 8\p@ \@plus2\p@ \@minus4\p@
+ \itemsep0\p@}
+\let\@listi\@listI
+\@listi
+\def\@listii {\leftmargin\leftmarginii
+ \labelwidth\leftmarginii
+ \advance\labelwidth-\labelsep
+ \topsep 0\p@ \@plus2\p@ \@minus\p@}
+\def\@listiii{\leftmargin\leftmarginiii
+ \labelwidth\leftmarginiii
+ \advance\labelwidth-\labelsep
+ \topsep 0\p@ \@plus\p@\@minus\p@
+ \parsep \z@
+ \partopsep \p@ \@plus\z@ \@minus\p@}
+
+\renewcommand\labelitemi{\normalfont\bfseries --}
+\renewcommand\labelitemii{$\m at th\bullet$}
+
+\setlength\arraycolsep{1.4\p@}
+\setlength\tabcolsep{1.4\p@}
+
+\def\tableofcontents{\chapter*{\contentsname\@mkboth{{\contentsname}}%
+ {{\contentsname}}}
+ \def\authcount##1{\setcounter{auco}{##1}\setcounter{@auth}{1}}
+ \def\lastand{\ifnum\value{auco}=2\relax
+ \unskip{} \andname\
+ \else
+ \unskip \lastandname\
+ \fi}%
+ \def\and{\stepcounter{@auth}\relax
+ \ifnum\value{@auth}=\value{auco}%
+ \lastand
+ \else
+ \unskip,
+ \fi}%
+ \@starttoc{toc}\if at restonecol\twocolumn\fi}
+
+\def\l at part#1#2{\addpenalty{\@secpenalty}%
+ \addvspace{2em plus\p@}% % space above part line
+ \begingroup
+ \parindent \z@
+ \rightskip \z@ plus 5em
+ \hrule\vskip5pt
+ \large % same size as for a contribution heading
+ \bfseries\boldmath % set line in boldface
+ \leavevmode % TeX command to enter horizontal mode.
+ #1\par
+ \vskip5pt
+ \hrule
+ \vskip1pt
+ \nobreak % Never break after part entry
+ \endgroup}
+
+\def\@dotsep{2}
+
+\def\hyperhrefextend{\ifx\hyper at anchor\@undefined\else
+{chapter.\thechapter}\fi}
+
+\def\addnumcontentsmark#1#2#3{%
+\addtocontents{#1}{\protect\contentsline{#2}{\protect\numberline
+ {\thechapter}#3}{\thepage}\hyperhrefextend}}
+\def\addcontentsmark#1#2#3{%
+\addtocontents{#1}{\protect\contentsline{#2}{#3}{\thepage}\hyperhrefextend}}
+\def\addcontentsmarkwop#1#2#3{%
+\addtocontents{#1}{\protect\contentsline{#2}{#3}{0}\hyperhrefextend}}
+
+\def\@adcmk[#1]{\ifcase #1 \or
+\def\@gtempa{\addnumcontentsmark}%
+ \or \def\@gtempa{\addcontentsmark}%
+ \or \def\@gtempa{\addcontentsmarkwop}%
+ \fi\@gtempa{toc}{chapter}}
+\def\addtocmark{\@ifnextchar[{\@adcmk}{\@adcmk[3]}}
+
+\def\l at chapter#1#2{\addpenalty{-\@highpenalty}
+ \vskip 1.0em plus 1pt \@tempdima 1.5em \begingroup
+ \parindent \z@ \rightskip \@tocrmarg
+ \advance\rightskip by 0pt plus 2cm
+ \parfillskip -\rightskip \pretolerance=10000
+ \leavevmode \advance\leftskip\@tempdima \hskip -\leftskip
+ {\large\bfseries\boldmath#1}\ifx0#2\hfil\null
+ \else
+ \nobreak
+ \leaders\hbox{$\m at th \mkern \@dotsep mu.\mkern
+ \@dotsep mu$}\hfill
+ \nobreak\hbox to\@pnumwidth{\hss #2}%
+ \fi\par
+ \penalty\@highpenalty \endgroup}
+
+\def\l at title#1#2{\addpenalty{-\@highpenalty}
+ \addvspace{8pt plus 1pt}
+ \@tempdima \z@
+ \begingroup
+ \parindent \z@ \rightskip \@tocrmarg
+ \advance\rightskip by 0pt plus 2cm
+ \parfillskip -\rightskip \pretolerance=10000
+ \leavevmode \advance\leftskip\@tempdima \hskip -\leftskip
+ #1\nobreak
+ \leaders\hbox{$\m at th \mkern \@dotsep mu.\mkern
+ \@dotsep mu$}\hfill
+ \nobreak\hbox to\@pnumwidth{\hss #2}\par
+ \penalty\@highpenalty \endgroup}
+
+\def\l at author#1#2{\addpenalty{\@highpenalty}
+ \@tempdima=\z@ %15\p@
+ \begingroup
+ \parindent \z@ \rightskip \@tocrmarg
+ \advance\rightskip by 0pt plus 2cm
+ \pretolerance=10000
+ \leavevmode \advance\leftskip\@tempdima %\hskip -\leftskip
+ \textit{#1}\par
+ \penalty\@highpenalty \endgroup}
+
+\setcounter{tocdepth}{0}
+\newdimen\tocchpnum
+\newdimen\tocsecnum
+\newdimen\tocsectotal
+\newdimen\tocsubsecnum
+\newdimen\tocsubsectotal
+\newdimen\tocsubsubsecnum
+\newdimen\tocsubsubsectotal
+\newdimen\tocparanum
+\newdimen\tocparatotal
+\newdimen\tocsubparanum
+\tocchpnum=\z@ % no chapter numbers
+\tocsecnum=15\p@ % section 88. plus 2.222pt
+\tocsubsecnum=23\p@ % subsection 88.8 plus 2.222pt
+\tocsubsubsecnum=27\p@ % subsubsection 88.8.8 plus 1.444pt
+\tocparanum=35\p@ % paragraph 88.8.8.8 plus 1.666pt
+\tocsubparanum=43\p@ % subparagraph 88.8.8.8.8 plus 1.888pt
+\def\calctocindent{%
+\tocsectotal=\tocchpnum
+\advance\tocsectotal by\tocsecnum
+\tocsubsectotal=\tocsectotal
+\advance\tocsubsectotal by\tocsubsecnum
+\tocsubsubsectotal=\tocsubsectotal
+\advance\tocsubsubsectotal by\tocsubsubsecnum
+\tocparatotal=\tocsubsubsectotal
+\advance\tocparatotal by\tocparanum}
+\calctocindent
+
+\def\l at section{\@dottedtocline{1}{\tocchpnum}{\tocsecnum}}
+\def\l at subsection{\@dottedtocline{2}{\tocsectotal}{\tocsubsecnum}}
+\def\l at subsubsection{\@dottedtocline{3}{\tocsubsectotal}{\tocsubsubsecnum}}
+\def\l at paragraph{\@dottedtocline{4}{\tocsubsubsectotal}{\tocparanum}}
+\def\l at subparagraph{\@dottedtocline{5}{\tocparatotal}{\tocsubparanum}}
+
+\def\listoffigures{\@restonecolfalse\if at twocolumn\@restonecoltrue\onecolumn
+ \fi\section*{\listfigurename\@mkboth{{\listfigurename}}{{\listfigurename}}}
+ \@starttoc{lof}\if at restonecol\twocolumn\fi}
+\def\l at figure{\@dottedtocline{1}{0em}{1.5em}}
+
+\def\listoftables{\@restonecolfalse\if at twocolumn\@restonecoltrue\onecolumn
+ \fi\section*{\listtablename\@mkboth{{\listtablename}}{{\listtablename}}}
+ \@starttoc{lot}\if at restonecol\twocolumn\fi}
+\let\l at table\l at figure
+
+\renewcommand\listoffigures{%
+ \section*{\listfigurename
+ \@mkboth{\listfigurename}{\listfigurename}}%
+ \@starttoc{lof}%
+ }
+
+\renewcommand\listoftables{%
+ \section*{\listtablename
+ \@mkboth{\listtablename}{\listtablename}}%
+ \@starttoc{lot}%
+ }
+
+\ifx\oribibl\undefined
+\ifx\citeauthoryear\undefined
+\renewenvironment{thebibliography}[1]
+ {\section*{\refname}
+ \def\@biblabel##1{##1.}
+ \small
+ \list{\@biblabel{\@arabic\c at enumiv}}%
+ {\settowidth\labelwidth{\@biblabel{#1}}%
+ \leftmargin\labelwidth
+ \advance\leftmargin\labelsep
+ \if at openbib
+ \advance\leftmargin\bibindent
+ \itemindent -\bibindent
+ \listparindent \itemindent
+ \parsep \z@
+ \fi
+ \usecounter{enumiv}%
+ \let\p at enumiv\@empty
+ \renewcommand\theenumiv{\@arabic\c at enumiv}}%
+ \if at openbib
+ \renewcommand\newblock{\par}%
+ \else
+ \renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
+ \fi
+ \sloppy\clubpenalty4000\widowpenalty4000%
+ \sfcode`\.=\@m}
+ {\def\@noitemerr
+ {\@latex at warning{Empty `thebibliography' environment}}%
+ \endlist}
+\def\@lbibitem[#1]#2{\item[{[#1]}\hfill]\if at filesw
+ {\let\protect\noexpand\immediate
+ \write\@auxout{\string\bibcite{#2}{#1}}}\fi\ignorespaces}
+\newcount\@tempcntc
+\def\@citex[#1]#2{\if at filesw\immediate\write\@auxout{\string\citation{#2}}\fi
+ \@tempcnta\z@\@tempcntb\m at ne\def\@citea{}\@cite{\@for\@citeb:=#2\do
+ {\@ifundefined
+ {b@\@citeb}{\@citeo\@tempcntb\m at ne\@citea\def\@citea{,}{\bfseries
+ ?}\@warning
+ {Citation `\@citeb' on page \thepage \space undefined}}%
+ {\setbox\z@\hbox{\global\@tempcntc0\csname b@\@citeb\endcsname\relax}%
+ \ifnum\@tempcntc=\z@ \@citeo\@tempcntb\m at ne
+ \@citea\def\@citea{,}\hbox{\csname b@\@citeb\endcsname}%
+ \else
+ \advance\@tempcntb\@ne
+ \ifnum\@tempcntb=\@tempcntc
+ \else\advance\@tempcntb\m at ne\@citeo
+ \@tempcnta\@tempcntc\@tempcntb\@tempcntc\fi\fi}}\@citeo}{#1}}
+\def\@citeo{\ifnum\@tempcnta>\@tempcntb\else
+ \@citea\def\@citea{,\,\hskip\z at skip}%
+ \ifnum\@tempcnta=\@tempcntb\the\@tempcnta\else
+ {\advance\@tempcnta\@ne\ifnum\@tempcnta=\@tempcntb \else
+ \def\@citea{--}\fi
+ \advance\@tempcnta\m at ne\the\@tempcnta\@citea\the\@tempcntb}\fi\fi}
+\else
+\renewenvironment{thebibliography}[1]
+ {\section*{\refname}
+ \small
+ \list{}%
+ {\settowidth\labelwidth{}%
+ \leftmargin\parindent
+ \itemindent=-\parindent
+ \labelsep=\z@
+ \if at openbib
+ \advance\leftmargin\bibindent
+ \itemindent -\bibindent
+ \listparindent \itemindent
+ \parsep \z@
+ \fi
+ \usecounter{enumiv}%
+ \let\p at enumiv\@empty
+ \renewcommand\theenumiv{}}%
+ \if at openbib
+ \renewcommand\newblock{\par}%
+ \else
+ \renewcommand\newblock{\hskip .11em \@plus.33em \@minus.07em}%
+ \fi
+ \sloppy\clubpenalty4000\widowpenalty4000%
+ \sfcode`\.=\@m}
+ {\def\@noitemerr
+ {\@latex at warning{Empty `thebibliography' environment}}%
+ \endlist}
+ \def\@cite#1{#1}%
+ \def\@lbibitem[#1]#2{\item[]\if at filesw
+ {\def\protect##1{\string ##1\space}\immediate
+ \write\@auxout{\string\bibcite{#2}{#1}}}\fi\ignorespaces}
+ \fi
+\else
+\@cons\@openbib at code{\noexpand\small}
+\fi
+
+\def\idxquad{\hskip 10\p@}% space that divides entry from number
+
+\def\@idxitem{\par\hangindent 10\p@}
+
+\def\subitem{\par\setbox0=\hbox{--\enspace}% second order
+ \noindent\hangindent\wd0\box0}% index entry
+
+\def\subsubitem{\par\setbox0=\hbox{--\,--\enspace}% third
+ \noindent\hangindent\wd0\box0}% order index entry
+
+\def\indexspace{\par \vskip 10\p@ plus5\p@ minus3\p@\relax}
+
+\renewenvironment{theindex}
+ {\@mkboth{\indexname}{\indexname}%
+ \thispagestyle{empty}\parindent\z@
+ \parskip\z@ \@plus .3\p@\relax
+ \let\item\par
+ \def\,{\relax\ifmmode\mskip\thinmuskip
+ \else\hskip0.2em\ignorespaces\fi}%
+ \normalfont\small
+ \begin{multicols}{2}[\@makeschapterhead{\indexname}]%
+ }
+ {\end{multicols}}
+
+\renewcommand\footnoterule{%
+ \kern-3\p@
+ \hrule\@width 2truecm
+ \kern2.6\p@}
+ \newdimen\fnindent
+ \fnindent1em
+\long\def\@makefntext#1{%
+ \parindent \fnindent%
+ \leftskip \fnindent%
+ \noindent
+ \llap{\hb at xt@1em{\hss\@makefnmark\ }}\ignorespaces#1}
+
+\long\def\@makecaption#1#2{%
+ \vskip\abovecaptionskip
+ \sbox\@tempboxa{{\bfseries #1.} #2}%
+ \ifdim \wd\@tempboxa >\hsize
+ {\bfseries #1.} #2\par
+ \else
+ \global \@minipagefalse
+ \hb at xt@\hsize{\hfil\box\@tempboxa\hfil}%
+ \fi
+ \vskip\belowcaptionskip}
+
+\def\fps at figure{htbp}
+\def\fnum at figure{\figurename\thinspace\thefigure}
+\def \@floatboxreset {%
+ \reset at font
+ \small
+ \@setnobreak
+ \@setminipage
+}
+\def\fps at table{htbp}
+\def\fnum at table{\tablename~\thetable}
+\renewenvironment{table}
+ {\setlength\abovecaptionskip{0\p@}%
+ \setlength\belowcaptionskip{10\p@}%
+ \@float{table}}
+ {\end at float}
+\renewenvironment{table*}
+ {\setlength\abovecaptionskip{0\p@}%
+ \setlength\belowcaptionskip{10\p@}%
+ \@dblfloat{table}}
+ {\end at dblfloat}
+
+\long\def\@caption#1[#2]#3{\par\addcontentsline{\csname
+ ext@#1\endcsname}{#1}{\protect\numberline{\csname
+ the#1\endcsname}{\ignorespaces #2}}\begingroup
+ \@parboxrestore
+ \@makecaption{\csname fnum@#1\endcsname}{\ignorespaces #3}\par
+ \endgroup}
+
+% LaTeX does not provide a command to enter the authors institute
+% addresses. The \institute command is defined here.
+
+\newcounter{@inst}
+\newcounter{@auth}
+\newcounter{auco}
+\newdimen\instindent
+\newbox\authrun
+\newtoks\authorrunning
+\newtoks\tocauthor
+\newbox\titrun
+\newtoks\titlerunning
+\newtoks\toctitle
+
+\def\clearheadinfo{\gdef\@author{No Author Given}%
+ \gdef\@title{No Title Given}%
+ \gdef\@subtitle{}%
+ \gdef\@institute{No Institute Given}%
+ \gdef\@thanks{}%
+ \global\titlerunning={}\global\authorrunning={}%
+ \global\toctitle={}\global\tocauthor={}}
+
+\def\institute#1{\gdef\@institute{#1}}
+
+\def\institutename{\par
+ \begingroup
+ \parskip=\z@
+ \parindent=\z@
+ \setcounter{@inst}{1}%
+ \def\and{\par\stepcounter{@inst}%
+ \noindent$^{\the at inst}$\enspace\ignorespaces}%
+ \setbox0=\vbox{\def\thanks##1{}\@institute}%
+ \ifnum\c@@inst=1\relax
+ \gdef\fnnstart{0}%
+ \else
+ \xdef\fnnstart{\c@@inst}%
+ \setcounter{@inst}{1}%
+ \noindent$^{\the at inst}$\enspace
+ \fi
+ \ignorespaces
+ \@institute\par
+ \endgroup}
+
+\def\@fnsymbol#1{\ensuremath{\ifcase#1\or\star\or{\star\star}\or
+ {\star\star\star}\or \dagger\or \ddagger\or
+ \mathchar "278\or \mathchar "27B\or \|\or **\or \dagger\dagger
+ \or \ddagger\ddagger \else\@ctrerr\fi}}
+
+\def\inst#1{\unskip$^{#1}$}
+\def\fnmsep{\unskip$^,$}
+\def\email#1{{\tt#1}}
+\AtBeginDocument{\@ifundefined{url}{\def\url#1{#1}}{}%
+\@ifpackageloaded{babel}{%
+\@ifundefined{extrasenglish}{}{\addto\extrasenglish{\switcht at albion}}%
+\@ifundefined{extrasfrenchb}{}{\addto\extrasfrenchb{\switcht at francais}}%
+\@ifundefined{extrasgerman}{}{\addto\extrasgerman{\switcht at deutsch}}%
+}{\switcht@@therlang}%
+}
+\def\homedir{\~{ }}
+
+\def\subtitle#1{\gdef\@subtitle{#1}}
+\clearheadinfo
+
+\renewcommand\maketitle{\newpage
+ \refstepcounter{chapter}%
+ \stepcounter{section}%
+ \setcounter{section}{0}%
+ \setcounter{subsection}{0}%
+ \setcounter{figure}{0}
+ \setcounter{table}{0}
+ \setcounter{equation}{0}
+ \setcounter{footnote}{0}%
+ \begingroup
+ \parindent=\z@
+ \renewcommand\thefootnote{\@fnsymbol\c at footnote}%
+ \if at twocolumn
+ \ifnum \col at number=\@ne
+ \@maketitle
+ \else
+ \twocolumn[\@maketitle]%
+ \fi
+ \else
+ \newpage
+ \global\@topnum\z@ % Prevents figures from going at top of page.
+ \@maketitle
+ \fi
+ \thispagestyle{empty}\@thanks
+%
+ \def\\{\unskip\ \ignorespaces}\def\inst##1{\unskip{}}%
+ \def\thanks##1{\unskip{}}\def\fnmsep{\unskip}%
+ \instindent=\hsize
+ \advance\instindent by-\headlineindent
+ \if!\the\toctitle!\addcontentsline{toc}{title}{\@title}\else
+ \addcontentsline{toc}{title}{\the\toctitle}\fi
+ \if at runhead
+ \if!\the\titlerunning!\else
+ \edef\@title{\the\titlerunning}%
+ \fi
+ \global\setbox\titrun=\hbox{\small\rm\unboldmath\ignorespaces\@title}%
+ \ifdim\wd\titrun>\instindent
+ \typeout{Title too long for running head. Please supply}%
+ \typeout{a shorter form with \string\titlerunning\space prior to
+ \string\maketitle}%
+ \global\setbox\titrun=\hbox{\small\rm
+ Title Suppressed Due to Excessive Length}%
+ \fi
+ \xdef\@title{\copy\titrun}%
+ \fi
+%
+ \if!\the\tocauthor!\relax
+ {\def\and{\noexpand\protect\noexpand\and}%
+ \protected at xdef\toc at uthor{\@author}}%
+ \else
+ \def\\{\noexpand\protect\noexpand\newline}%
+ \protected at xdef\scratch{\the\tocauthor}%
+ \protected at xdef\toc at uthor{\scratch}%
+ \fi
+ \addcontentsline{toc}{author}{\toc at uthor}%
+ \if at runhead
+ \if!\the\authorrunning!
+ \value{@inst}=\value{@auth}%
+ \setcounter{@auth}{1}%
+ \else
+ \edef\@author{\the\authorrunning}%
+ \fi
+ \global\setbox\authrun=\hbox{\small\unboldmath\@author\unskip}%
+ \ifdim\wd\authrun>\instindent
+ \typeout{Names of authors too long for running head. Please supply}%
+ \typeout{a shorter form with \string\authorrunning\space prior to
+ \string\maketitle}%
+ \global\setbox\authrun=\hbox{\small\rm
+ Authors Suppressed Due to Excessive Length}%
+ \fi
+ \xdef\@author{\copy\authrun}%
+ \markboth{\@author}{\@title}%
+ \fi
+ \endgroup
+ \setcounter{footnote}{\fnnstart}%
+ \clearheadinfo}
+%
+\def\@maketitle{\newpage
+ \markboth{}{}%
+ \def\lastand{\ifnum\value{@inst}=2\relax
+ \unskip{} \andname\
+ \else
+ \unskip \lastandname\
+ \fi}%
+ \def\and{\stepcounter{@auth}\relax
+ \ifnum\value{@auth}=\value{@inst}%
+ \lastand
+ \else
+ \unskip,
+ \fi}%
+ \begin{center}%
+ \let\newline\\
+ {\Large \bfseries\boldmath
+ \pretolerance=10000
+ \@title \par}\vskip .8cm
+\if!\@subtitle!\else {\large \bfseries\boldmath
+ \vskip -.65cm
+ \pretolerance=10000
+ \@subtitle \par}\vskip .8cm\fi
+ \setbox0=\vbox{\setcounter{@auth}{1}\def\and{\stepcounter{@auth}}%
+ \def\thanks##1{}\@author}%
+ \global\value{@inst}=\value{@auth}%
+ \global\value{auco}=\value{@auth}%
+ \setcounter{@auth}{1}%
+{\lineskip .5em
+\noindent\ignorespaces
+\@author\vskip.35cm}
+ {\small\institutename}
+ \end{center}%
+ }
+
+% definition of the "\spnewtheorem" command.
+%
+% Usage:
+%
+% \spnewtheorem{env_nam}{caption}[within]{cap_font}{body_font}
+% or \spnewtheorem{env_nam}[numbered_like]{caption}{cap_font}{body_font}
+% or \spnewtheorem*{env_nam}{caption}{cap_font}{body_font}
+%
+% New is "cap_font" and "body_font". It stands for
+% fontdefinition of the caption and the text itself.
+%
+% "\spnewtheorem*" gives a theorem without number.
+%
+% A defined spnewthoerem environment is used as described
+% by Lamport.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\def\@thmcountersep{}
+\def\@thmcounterend{.}
+
+\def\spnewtheorem{\@ifstar{\@sthm}{\@Sthm}}
+
+% definition of \spnewtheorem with number
+
+\def\@spnthm#1#2{%
+ \@ifnextchar[{\@spxnthm{#1}{#2}}{\@spynthm{#1}{#2}}}
+\def\@Sthm#1{\@ifnextchar[{\@spothm{#1}}{\@spnthm{#1}}}
+
+\def\@spxnthm#1#2[#3]#4#5{\expandafter\@ifdefinable\csname #1\endcsname
+ {\@definecounter{#1}\@addtoreset{#1}{#3}%
+ \expandafter\xdef\csname the#1\endcsname{\expandafter\noexpand
+ \csname the#3\endcsname \noexpand\@thmcountersep \@thmcounter{#1}}%
+ \expandafter\xdef\csname #1name\endcsname{#2}%
+ \global\@namedef{#1}{\@spthm{#1}{\csname #1name\endcsname}{#4}{#5}}%
+ \global\@namedef{end#1}{\@endtheorem}}}
+
+\def\@spynthm#1#2#3#4{\expandafter\@ifdefinable\csname #1\endcsname
+ {\@definecounter{#1}%
+ \expandafter\xdef\csname the#1\endcsname{\@thmcounter{#1}}%
+ \expandafter\xdef\csname #1name\endcsname{#2}%
+ \global\@namedef{#1}{\@spthm{#1}{\csname #1name\endcsname}{#3}{#4}}%
+ \global\@namedef{end#1}{\@endtheorem}}}
+
+\def\@spothm#1[#2]#3#4#5{%
+ \@ifundefined{c@#2}{\@latexerr{No theorem environment `#2' defined}\@eha}%
+ {\expandafter\@ifdefinable\csname #1\endcsname
+ {\global\@namedef{the#1}{\@nameuse{the#2}}%
+ \expandafter\xdef\csname #1name\endcsname{#3}%
+ \global\@namedef{#1}{\@spthm{#2}{\csname #1name\endcsname}{#4}{#5}}%
+ \global\@namedef{end#1}{\@endtheorem}}}}
+
+\def\@spthm#1#2#3#4{\topsep 7\p@ \@plus2\p@ \@minus4\p@
+\refstepcounter{#1}%
+\@ifnextchar[{\@spythm{#1}{#2}{#3}{#4}}{\@spxthm{#1}{#2}{#3}{#4}}}
+
+\def\@spxthm#1#2#3#4{\@spbegintheorem{#2}{\csname the#1\endcsname}{#3}{#4}%
+ \ignorespaces}
+
+\def\@spythm#1#2#3#4[#5]{\@spopargbegintheorem{#2}{\csname
+ the#1\endcsname}{#5}{#3}{#4}\ignorespaces}
+
+\def\@spbegintheorem#1#2#3#4{\trivlist
+ \item[\hskip\labelsep{#3#1\ #2\@thmcounterend}]#4}
+
+\def\@spopargbegintheorem#1#2#3#4#5{\trivlist
+ \item[\hskip\labelsep{#4#1\ #2}]{#4(#3)\@thmcounterend\ }#5}
+
+% definition of \spnewtheorem* without number
+
+\def\@sthm#1#2{\@Ynthm{#1}{#2}}
+
+\def\@Ynthm#1#2#3#4{\expandafter\@ifdefinable\csname #1\endcsname
+ {\global\@namedef{#1}{\@Thm{\csname #1name\endcsname}{#3}{#4}}%
+ \expandafter\xdef\csname #1name\endcsname{#2}%
+ \global\@namedef{end#1}{\@endtheorem}}}
+
+\def\@Thm#1#2#3{\topsep 7\p@ \@plus2\p@ \@minus4\p@
+\@ifnextchar[{\@Ythm{#1}{#2}{#3}}{\@Xthm{#1}{#2}{#3}}}
+
+\def\@Xthm#1#2#3{\@Begintheorem{#1}{#2}{#3}\ignorespaces}
+
+\def\@Ythm#1#2#3[#4]{\@Opargbegintheorem{#1}
+ {#4}{#2}{#3}\ignorespaces}
+
+\def\@Begintheorem#1#2#3{#3\trivlist
+ \item[\hskip\labelsep{#2#1\@thmcounterend}]}
+
+\def\@Opargbegintheorem#1#2#3#4{#4\trivlist
+ \item[\hskip\labelsep{#3#1}]{#3(#2)\@thmcounterend\ }}
+
+\if at envcntsect
+ \def\@thmcountersep{.}
+ \spnewtheorem{theorem}{Theorem}[section]{\bfseries}{\itshape}
+\else
+ \spnewtheorem{theorem}{Theorem}{\bfseries}{\itshape}
+ \if at envcntreset
+ \@addtoreset{theorem}{section}
+ \else
+ \@addtoreset{theorem}{chapter}
+ \fi
+\fi
+
+%definition of divers theorem environments
+\spnewtheorem*{claim}{Claim}{\itshape}{\rmfamily}
+\spnewtheorem*{proof}{Proof}{\itshape}{\rmfamily}
+\if at envcntsame % alle Umgebungen wie Theorem.
+ \def\spn at wtheorem#1#2#3#4{\@spothm{#1}[theorem]{#2}{#3}{#4}}
+\else % alle Umgebungen mit eigenem Zaehler
+ \if at envcntsect % mit section numeriert
+ \def\spn at wtheorem#1#2#3#4{\@spxnthm{#1}{#2}[section]{#3}{#4}}
+ \else % nicht mit section numeriert
+ \if at envcntreset
+ \def\spn at wtheorem#1#2#3#4{\@spynthm{#1}{#2}{#3}{#4}
+ \@addtoreset{#1}{section}}
+ \else
+ \def\spn at wtheorem#1#2#3#4{\@spynthm{#1}{#2}{#3}{#4}
+ \@addtoreset{#1}{chapter}}%
+ \fi
+ \fi
+\fi
+\spn at wtheorem{case}{Case}{\itshape}{\rmfamily}
+\spn at wtheorem{conjecture}{Conjecture}{\itshape}{\rmfamily}
+\spn at wtheorem{corollary}{Corollary}{\bfseries}{\itshape}
+\spn at wtheorem{definition}{Definition}{\bfseries}{\itshape}
+\spn at wtheorem{example}{Example}{\itshape}{\rmfamily}
+\spn at wtheorem{exercise}{Exercise}{\itshape}{\rmfamily}
+\spn at wtheorem{lemma}{Lemma}{\bfseries}{\itshape}
+\spn at wtheorem{note}{Note}{\itshape}{\rmfamily}
+\spn at wtheorem{problem}{Problem}{\itshape}{\rmfamily}
+\spn at wtheorem{property}{Property}{\itshape}{\rmfamily}
+\spn at wtheorem{proposition}{Proposition}{\bfseries}{\itshape}
+\spn at wtheorem{question}{Question}{\itshape}{\rmfamily}
+\spn at wtheorem{solution}{Solution}{\itshape}{\rmfamily}
+\spn at wtheorem{remark}{Remark}{\itshape}{\rmfamily}
+
+\def\@takefromreset#1#2{%
+ \def\@tempa{#1}%
+ \let\@tempd\@elt
+ \def\@elt##1{%
+ \def\@tempb{##1}%
+ \ifx\@tempa\@tempb\else
+ \@addtoreset{##1}{#2}%
+ \fi}%
+ \expandafter\expandafter\let\expandafter\@tempc\csname cl@#2\endcsname
+ \expandafter\def\csname cl@#2\endcsname{}%
+ \@tempc
+ \let\@elt\@tempd}
+
+\def\theopargself{\def\@spopargbegintheorem##1##2##3##4##5{\trivlist
+ \item[\hskip\labelsep{##4##1\ ##2}]{##4##3\@thmcounterend\ }##5}
+ \def\@Opargbegintheorem##1##2##3##4{##4\trivlist
+ \item[\hskip\labelsep{##3##1}]{##3##2\@thmcounterend\ }}
+ }
+
+\renewenvironment{abstract}{%
+ \list{}{\advance\topsep by0.35cm\relax\small
+ \leftmargin=1cm
+ \labelwidth=\z@
+ \listparindent=\z@
+ \itemindent\listparindent
+ \rightmargin\leftmargin}\item[\hskip\labelsep
+ \bfseries\abstractname]}
+ {\endlist}
+
+\newdimen\headlineindent % dimension for space between
+\headlineindent=1.166cm % number and text of headings.
+
+\def\ps at headings{\let\@mkboth\@gobbletwo
+ \let\@oddfoot\@empty\let\@evenfoot\@empty
+ \def\@evenhead{\normalfont\small\rlap{\thepage}\hspace{\headlineindent}%
+ \leftmark\hfil}
+ \def\@oddhead{\normalfont\small\hfil\rightmark\hspace{\headlineindent}%
+ \llap{\thepage}}
+ \def\chaptermark##1{}%
+ \def\sectionmark##1{}%
+ \def\subsectionmark##1{}}
+
+\def\ps at titlepage{\let\@mkboth\@gobbletwo
+ \let\@oddfoot\@empty\let\@evenfoot\@empty
+ \def\@evenhead{\normalfont\small\rlap{\thepage}\hspace{\headlineindent}%
+ \hfil}
+ \def\@oddhead{\normalfont\small\hfil\hspace{\headlineindent}%
+ \llap{\thepage}}
+ \def\chaptermark##1{}%
+ \def\sectionmark##1{}%
+ \def\subsectionmark##1{}}
+
+\if at runhead\ps at headings\else
+\ps at empty\fi
+
+\setlength\arraycolsep{1.4\p@}
+\setlength\tabcolsep{1.4\p@}
+
+\endinput
+%end of file llncs.cls
Added: trunk/community/papers/05_biomed_bio/paper-text.tex
===================================================================
--- trunk/community/papers/05_biomed_bio/paper-text.tex (rev 0)
+++ trunk/community/papers/05_biomed_bio/paper-text.tex 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,887 @@
+\begin{abstract}
+ The development of Free Software has much in common with scientific
+ research: the sharing of knowledge and to make progress.
+
+ Software in science co-evolves with data that is available to feed
+ it. In the data driven molecular sciences, the information
+ technology is particularly concerned to ease the data flow between
+ applications. This is of particular importance because of the
+ biological data's heterogeneity while individual entries are
+ strongly semantically interdependent. Bioinformatics has developed
+ technologies to communicate between data and tools.
+
+ With agent and grid technologies, Computer Science has developed
+ means to operate across multiple databases, hereto also connecting
+ otherwise independent institutes across the world. For the agent
+ community for the access of standard technologies and databases, and
+ for the grid technologies in particular, a common problem is the
+ accessibility of information sources in respective local
+ installations. These may differ in version, location or access
+ permissions. Because of these differences, a common infrastructure
+ still requires considerable local maintenance, particularly for the
+ incorporation of novel data sources.
+
+ For computational grids, VOs determine installation paths and
+ inter-institutional access permissions. The actual work for implementing
+ such a agreements is imposed on the respective site's maintainer.
+ A further unresolved issue is the
+ heterogeneity of underlying hardware. This paper describes
+ Debian-Med, a special interest group within the Debian Linux
+ organisation, aiming to provide a hardware-independent common view
+ on Free software and databases for medical and biological research,
+ and stresses its possible impact on the community as a backbone of
+ grids and information agents in computational biology.
+\end{abstract}
+
+\begin{tabular}{ll} % to become llll later
+CDD& Custom Debian Distribution \\
+BOINC&Berkeley Open Infrastructure for Network Computing \\
+BTS& Bug Tracking System \\
+DFSG& Debian Free Software Guidelines \\
+EBI& European Bioinformatics Institute \\
+LSB& Linux Standard Base \\
+RE & Runtime Environment \\
+SETI& Search for Extraterrestrial Intelligence \\
+SRS& Sequence Retrieval System \\
+VO& Virtual Organisation \\
+\end{tabular}
+
+
+\section{Introduction}
+
+\subsection{Information integration in bioinformatics}
+
+The gold standard for the integration of information in bioinformatics
+today still is the SRS platform of Lion Bioscience as publicly accessible at the
+European Bioinformatics Institute (EBI) \cite{zdobnow:2002}.
+The developers take a particular pride in the flexibility of the tool,
+facilitating a straight-forward integration of local databases, a feature
+signing responsible for the commercial success of this technology far beyond
+its application in bioinformatics. While still available to the academic community
+for no money, the number of installations of SRS is surprisingly low. This
+speaks for the quality of the EBI installation, but to our understanding also for
+the extra burden such a system imposes in terms of maintenance. A companion tool, Prisma, addressing automated updates,
+is not free.
+
+The problem of maintenance and coherence across sites is particularly
+obvious in the myGrid effort \cite{stevens:2004}. The development of
+workflows for the repository of data and their analysis across
+multiple tools and sites is mostly static.
+It is not possible for a machine already contributing to myGrid that
+has idle time, to help out other machines that are busy by a dynamic
+addition of services to those it already offers.
+Such would at least require the installation and deinstallation of the
+service's respective runtime environment in a fully automated manner.
+Further problems would require to be addressed for the notification of
+other sites in order to become aware of such a change and to subsequently
+react to to it. Such issues are addressed in agent research and
+standardised middleware like CORBA. The here presented Debian Linux
+distribution has implemented such dynamics.
+
+The sharing of workloads in homogeneous environments is
+addressed by grid initiatives, like by the
+\printurl{www.globus.org}{Globus}-based \cite{foster:2001}
+\printurl{www.nordugrid.org}{NorduGrid} initiative\cite{eerola:2004}.
+For each site, the workload is addressed by one or multiple clusters
+of homogeneous machines, the coherence of installations across
+institutions is coordinated and supervised by so called virtual
+organisations (VOs). Those define Runtime Environments (REs)
+and clusters adhering to such specify such in their description
+that is utilised in the selection of clusters feasible for
+a job's execution.
+
+To deploy one's algorithms and data, the programs
+are submitted as source code and (unless programmed in
+interpreted scripts or other hardware-independent languages)
+compiled prior to execution. VOs may ease this burden and require the
+sites to install a minimal set of programs for every machine by the
+inclusion on an RE. While this has been proven to be very functional for
+the grids' roots in particle physics, for bioinformatics, with its vast
+heterogeneity of small applications and comparatively tiny databases,
+even if an agreement could possibly be reached in a VO, the effect could
+hardly be maintained by a site's maintainer.
+
+
+\subsection{Status of Free Software in Biology}
+
+Common programs like a web server, or a mail user agent are installed
+on most computers and have a very large user base.
+Knowing this, many gifted programmers feel obliged for
+this kind of Free Software - they just need it for their own and they
+know to make a difference to the world. So one
+finds a fast, growing community around Free Software packages
+that have a widespread use.
+For specialised software in general and particularly for biological software,
+one needs to first explain what a particular software does. Often the
+developers get their satisfaction not from the software but from the
+excitement of extra insights in biological processes - the beauty of which
+is likely not to be accessible to regular software enthusiasts.
+
+As a view shared by many in Open Source Bioinformatics, Ewan Birney of
+the EnsEMBL \cite{hubbard:2005} project stresses Open
+Source to "ensure scientific progress". He also laid out that the
+Open Source of programs is a comparatively trivial issue when compared
+with the openness of biological data. The latter is often far more
+expensive to produce. While giving the data away might possibly
+diminish one's competitive advantage, the sharing of a program with
+others and respective citations is well accepted as fostering one's
+career.
+
+
+\subsection{Debian, distributed computing, and bioinformatics}
+
+This paper presents a development from the Debian Linux Free Software community that
+offers solutions to the prior mentioned problems. The basic idea is to automate updates,
+to share maintenance load under governance of a peer controlled strict
+policy and to use asymmetric cryptography for the packages' integrity
+and authenticity. The underlying technology may be applied to any program
+and be run independently from Debian. The technology has been ported to
+11 different platforms, hence providing a considerable freedom in the
+selection of hardware.
+
+A subproject of Debian is Debian-Med\cite{tille:ltk03}, a
+\printurl{people.debian.org/\~tille/cdd}{Custom Debian
+ Distribution}\cite{tille:cdd}, supporting users with a special
+interest in medical and biological problems. The common goal of all
+CDDs is to make installation and administration of computers for their
+target users as easy as possible, and to serve in the role as the
+missing link between software developers and users well. The
+importance of this technology for computational grids and information
+agents has not been presented before.
+
+
+\section{Methods}
+
+
+\subsection{Unique technology supporting Debian's principles in packaging}
+
+
+\subsubsection{{\ttfamily .deb} packages}
+
+Most distributors ship their distribution in binary packages. Two
+package formats are widely used\cite{hess:2003}:
+
+\begin{description}
+\item[RPM (RedHat Package Manager)] which is supported by RedHat,
+ SuSE, Mandrake and others.
+\item[DEB (Debian Package)] used by Debian and derived distributions.
+\end{description}
+
+It is this {\itshape adherence to policy\/} that causes a distribution
+to remain consistent within its own bounds. At the same time, this is
+the reason why packages can not always be safely installed across
+distribution boundaries. A SuSE \file{package.rpm} might not play well
+with a RedHat \file{package.rpm}, although the packages work perfectly
+well within their own distributions. A similar compatibility problem
+could also apply to packages from the same distributor, but from a
+different version or generation of the distribution.
+
+For Debian, all files of a program are packed as the \command{ar}
+archiver, otherwise known for the creation of programming libraries.
+Every such DEB package has a companion source package from which the
+binary package may be built automatically.
+The distributions of SuSE, RedHat and derivatives use the RPM format.
+The program \command{alien} by Joey Hess (not to be mistaken for the
+Grid environment at CERN) can translate between these. Though scripts
+to be run upon installation may get lost in the translation process.
+
+
+\subsubsection{Build daemons}
+
+Sites external to the Debian main distribution may
+offer packages only for a subset of architectures.
+The Debian main distribution, however, automatically
+compiles software for all 11
+architectures that are supported by the Debian effort.
+To get a package into Debian, be it novel or an update of an existing package,
+the maintainer of a package submits the source code of the program together with his changes on the code to create the package. The build daemons (or autobuilders) compile the packages for each of the supported systems and make the resulting package publicly available for download. Logs of the build platforms are available online for everybody's inspection.
+
+
+\subsubsection{Bug tracking system}
+
+Users should give immediate feedback about problems arising in using a
+package. They always have the choice of reporting these to the
+upstream developer, usually per email. A particular strength of
+\printurl{www.sourceforge.net}{SourceForget.net} is to bring users of
+a particular software together. Earlier than this effort was the
+\printurl{www.debian.org/Bugs}{Debian Bug Tracking System} (BTS).
+The maintainer of a software can decide if the bug should be forwarded to the upstream
+developers of the package or if it is fixed by himself. All problems are made
+public and hence the whole community may contribute to solving a particular issue.
+
+
+\subsection{Divide and conquer of package maintenance}
+
+The Debian Project is an association of individuals who share the
+intention to create the best possible free operating system. This
+operating system that which is created is called Debian GNU/Linux, or
+simply Debian for short. Everybody in the internet may initiate a site
+and offer packages for the installation in Debian. A local administrator
+has to decide, if this public source may be trusted.
+
+For Free Software development to work it requires a critical mass of
+supporters. Development without feedback prior to the submission of the
+final product is disadvantageous. The development of programs is not the
+main concern of a regular Linux Distribution. However, with the focus
+on Free Software and smooth local compilation, Debian considerably eases
+the contribution of comments and concise feedback of the technically skilled
+early adopters. Debian such helps to bring developers and users of
+applications together.
+
+\begin{figure*}
+\centering
+\myinsertgraphic{earthkeyring}
+\caption{Debian web of trust}\label{figure:weboftrust}
+\end{figure*}
+
+All members of the Debian project are connected in a
+\printurl{people.debian.org/~edward/globe/earthkeyring}{web of trust},
+which is woven by signing GnuPG
+(\printurl{www.gnupg.org}{www.gnupg.org}) keys\ref{figure:weboftrust}.
+A central requirement to become a member of the Debian project is to
+have one's GPG key signed by an already accepted member of the Debian
+community. When Debian developers first meet in person, they sign
+each other's keys. Thus, the web of trust is woven.
+
+Debian does its best to have every member profit of somebody else's work as quickly as possible.
+
+\subsubsection{Debian Policy}
+
+All GNU/Linux distributions have a certain amount of common ground,
+and the \printurl{www.linuxbase.org/}{Linux Standard Base}
+(LSB)\cite{lsb} is attempting to develop and promote a set of
+standards that will increase compatibility among Linux distributions,
+hereby enabling software applications to run on any compliant system.
+The very essence of any distribution, (whether delivered as RPMs,
+DEBs, Source tarballs or ports) is the choice of {\itshape policy
+ statements\/}.
+
+\halfsloppy{\itshape Policy statements\/} in Debian\cite{debianpolicy}
+specify configuration files to reside in
+\Path{/etc/\$package/\$package.conf}, logfiles go to
+\Path{/var/log/\$package/\$package.log} and the documentation files to
+be located in \Path{/usr/share/doc/\$package}. CGI-scripts are
+installed in \Path{/usr/lib/cgi-bin}.
+
+The policy statements are followed by the tool-chains and
+libraries used to build the software, and the lists of dependencies, which
+dictate the prerequisites and order in which the software has to be
+built and installed.
+
+Policies in Debian are developed within the community. Commonly with
+a single person or a small team drafting it, with further refinements
+being discussed in respective mailing lists.
+
+While every single maintainer of a Debian package has to build the
+package in compliance with the policy he has the ability and the right
+to decide which software is worth packaging. Normally maintainers
+choose the software which is used in their own work and they are free
+to move the development of Debian in a certain direction (as long as
+they follow the rules of the policy). This is referred to as {\em
+ Do-o-cracy} in Debian which means: The doer decides what is done.
+
+\subsection{Selection of packages}
+
+Debian contains nearly 10000 binary packages, and this number is
+constantly increasing. There is no single user who needs all these
+packages. The regular user is interested in a subset of these packages.
+To specify packages of one's particular interest, several options are
+provided by Debian:
+\begin{description}
+\item[tasksel]
+ Provision of a reasonable selection of rather general tasks that can
+ be accomplished using a set of packages installed on a Debian
+ GNU/Linux system. However, these are not yet covering scientific
+ applications. The CDD toolkit which is currently developed will also
+ support \command{tasksel} to enable selecting for instance
+ Debian-Med right after a fresh installation of a general Debian
+ system.
+
+\item[standard package management]
+ \command{dpkg} and \command{apt} provide means to search for
+ packages of particular interest by its name or words in the
+ package's description. Every package also indicates, as set by its
+ maintainer, references to other packages of potential interest.
+\end{description}
+
+
+In its current development, an ontology of applications of software,
+upon which semantical queries could be performed, analogous to
+Moby-S and \printurl{www.biomoby.org}{BioMoby} \cite{lord:2004,wilkinson:2005}
+effort, is not available.
+
+A package management system is a very strong tool to manage software
+packages on your computer. A large amount of the work of a
+distributor is building these software packages.
+The Debian package management tools have been ported to
+MacOS X\cite{fink:2005} and other Linux Distributions\cite{kojima:2000}.
+
+Debian officially maintains 11 different architectures with many more
+not officially supported ports to other operating systems, which includes some
+that run another flavour of UNIX. Its
+technology for package management has been adopted for other operating
+systems, i.e. Fink on MacOSX
+(\printurl{fink.sourceforge.net}{fink.sourceforge.net}).
+
+
+A {\itshape distribution\/} is a collection of software packages around the
+GNU Linux operating system that satisfies the needs of the target user
+group. There are general distributions, which try to support all
+users, and there are several specialised distributions, which each
+target a special group of users.
+
+{\itshape Distributors\/} are those companies that are building these
+collections of software around the GNU Linux operating system.
+Since the software is Free, the user who buys a distribution pays for
+the service that the distributor is providing. These services might
+be:
+\begin{itemize}
+ \item Preparing a useful collection of software around GNU Linux.
+ \item Caring for smooth installation that the target user is able to
+ manage.
+ \item Providing software updates and security fixes.
+ \item Writing documentation and translations to enable the user to
+ use the distribution with maximum effect.
+ \item Selling Boxes with ready to install CDs and printed
+ documentation.
+ \item Offering training and qualification.
+\end{itemize}
+
+The best established Distributors of GNU/Linux systems are
+\printurl{www.mandrakelinux.com}{Mandrake},
+\printurl{www.redhat.com}{RedHat}, \printurl{www.suse.com}{SuSE} (now
+owned by \printurl{www.novell.com/linux}{Novell}) and
+\printurl{www.debian.org}{Debian}.
+\printurl{www.linspire.com}{Linspire},
+\printurl{www.xandros.com}{Xandros},
+\printurl{www.mepis.org}{MEPIS} and
+\printurl{www.ubuntulinux.org}{Ubuntu} are well known derivates of
+Debian.
+
+\section{Results}
+
+\subsection{Bioinformatics and Debian-associated repositories}
+
+
+\begin{description}
+
+\item[Bio-Linux Bioinformatics package repository]
+
+ \halfsloppy The Bio-Linux Bioinformatics package repository contains
+ the \printurl{envgen.nox.ac.uk/pkg\_repository.html}{Bio-Linux 4
+ bioinformatics software} and can be installed from a centralised
+ repository located on the EGTDC server. The packages available from
+ this site have been created by the EGTDC specifically for the
+ Bio-Linux project and are in deb format.
+
+ The projects claim to be compatible with any installation of Debian
+ or Debian variants. This might be a weak sentence because Debian
+ variants are quite different. It is better to say exactly Debian
+ "stable" or Debian "testing" and draw a line between native Debian
+ and perhaps commercial derivatives which might differ in certain
+ aspects.
+
+ The packages are not, however, core Debian packages. Please read the
+ notes below for further details about Bio-Linux packages. They add
+ the following notes:
+
+ \begin{enumerate}
+ \item \sloppy {\em All} of the packages have a dependency on the package
+ \package{bio-linux-base-directories}, as this is the package that
+ sets up the directory structure and dependencies of several of the
+ Bio-Linux system packages. This creates a number of directories
+ and configuration files for Bio-Linux but will NOT overwrite
+ anything on your system. Therefore you may wish to install this
+ package first, or force the install of other packages if you do
+ not want to install this package.
+ \item {\em Warning}: The \package{bio-linux-bldp-files} package
+ contains files which install to a folder called
+ \Path{/var/www/boinformatics}. Thus, please ensure that you do
+ not already have a directory on your system of this name, or that,
+ at the very least, you are not concerned with overwriting any
+ index.html file in such an existing directory.
+ \item All packages install to \Path{/usr/local/bioinf} and create
+ symlinks in \Path{/usr/local/bin} with the exception of the
+ bio-linux-genespring software which installs to
+ \Path{/home/db/SiliconGenetics} (for more information regarding
+ installation of GeneSpring, see our
+ \printurl{envgen.nox.ac.uk/sg.html}{GeneSpring Web Page}.)
+ \item \halfsloppy \package{Bio-linux-base-directories} installs two
+ files into \Path{/usr/local/bioinf/config\_files} (\Path{bioenvrc}
+ and \Path{aliasrc}). The file {\em \Path{bioenvrc} should be
+ sourced\/} by your shell if you want to pick up the correct
+ environmental variables for the software. We recommend the use of
+ the
+ \printurl{envgen.nox.ac.uk/envgen/software/archives/000499.html\#shells}{z-shell
+ for Bio-Linux}. You will also want to \command{source aliasrc}
+ if you wish to run some of the Java based software - for example
+ \command{maxdView}, \command{maxdLoad2}, \command{mesquite},
+ \command{forester}, etc. You will {\em also need to edit} the
+ \Path{aliasrc} file to reflect the location of the Java binaries
+ on your system.
+ \end{enumerate}
+
+ The authors did a great job in collecting a certain amount of very
+ useful software for biologists and the Debian-Med project might try
+ to include some packages which are not yet available in Debian
+ officially.
+
+
+\item[BioLinux-BR Project]
+
+ \halfsloppy A similar project is the
+ \printurl{biolinux.df.ibilce.unesp.br/index.en.php}{BioLinux-BR
+ Project} which is a project directed to the scientific community.
+ Their goal is to create a Linux distribution for people with little
+ familiarity with the installation of the operational system and
+ mainly for people who do not know to proceed unpacking a program,
+ compile and install it correctly.
+
+ For these reasons, they want to give contribution, developing a
+ Linux system that aims to be easy to use and still offering packages
+ that will be part of the BioLinux-BR. Giving this option, we will
+ not be compelling anybody to change its Linux distribution, since
+ there are packages developed for the greater Linux distributions.
+
+ "BR" here stands for "Brasil" which might lead to the assumption
+ that some internationalisation effort was done, but according to the
+ authors this was not their main concern but rather a side effect.
+
+ In fact, this project has assembled a huge amount of packages,
+ probably the most complete collection of Free Software in biology.
+ Packages for multiple distributions are provided, which includes
+ Debian, and a live CD.
+
+\item[bioinformatics.debian.net]
+
+ Debian developer Matt Hope has created a small set of packages for
+ Debian that he has not yet uploaded to the main distribution.
+ Most are in a very nice state he just should submit.
+
+\end{description}
+
+
+\subsection{Bioinformatics Live CDs}
+
+The concept of a live CD allows to create a CD or DVD that boots a
+computer, starts a defined set of application without a user's
+intervention and has all tools in place that suits a particular
+community. Such provide fully featured Linux workstations without
+additional installations of access to local disk space, alternatively
+booting via the network is supported by Debian, which particularly
+appeals to Blades or large clusters. The most successful such LiveCD
+is the Debian-derived Knoppix\cite{knopper:2005}.
+
+The descriptions below only summarise a few efforts but give insights
+into the vast realm of possibilities also for distributed computing.
+It should be pointed out that all Knoppix-derived\cite{knopper:2005}
+bioinformatics Live CDs may become members of the NorduGrid with the
+effort of Niels E. Larsen\cite{larsen:2005}, who provides a respective
+script to create a LiveCD that lets one immediately join a grid with
+4000+ CPUs\cite{larsenscript:2005}.
+
+\begin{description}
+\item[The Quantian Scientific Computing Environment]
+
+ Quantian is a remastering of a well established effort
+ (\printurl{www.knopper.net/knoppix/index-en.html}{Knoppix}). Recent
+ versions of Quantian \cite{eddelbuettel:quantian} are based on
+ \printurl{bofh.be/clusterknoppix/}{ClusterKnoppix
+ }\cite{vandersmissen:2005} and add support for
+ \printurl{www.openmosix.org}{OpenMosix} \cite{bar:openmosix},
+ including remote booting of light clients in an openMosix terminal
+ server context. Earlier releases are still available; see below for
+ URLs for downloads as well as ordering information. More detailed
+ information \printurl{dirk.eddelbuettel.com/quantian}{are
+ available at the Quantian homepage}.
+
+ The interesting part for biologists is that Quantian contains in
+ addition all interesting packages of Debian-Med. The author Dirk
+ Eddelbuettel, who is a Debian developer himself, just used the
+ simply to install biological software feature we provide and thus
+ made a great profit from Debian-Med.
+
+\item[Vigyaan - the biochemical software workbench]
+
+ \halfsloppy\printurl{www.vigyaancd.org}{Vigyaan} is an electronic
+ workbench for bioinformatics, computational biology and
+ computational chemistry. It has been designed to meet the needs of
+ both beginners and experts. VigyaanCD is a live Linux CD containing
+ all the required software to boot the computer with ready to use
+ modelling software. VigyaanCD v0.1 is based on Knoppix v3.3.
+
+ Vigyann contains some programs which are not yet contained in
+ Debian. It might be mutually beneficial to include these provided
+ that the license fits the DFSG.
+
+\item[BioKnoppix]
+
+
+ \printurl{bioknoppix.hpcf.upr.edu}{BioKnoppix} is a customised
+ distribution of Knoppix Linux Live CD. It is a very similar project
+ to the previous which specialises Knoppix for computational biology
+ and chemistry.
+
+
+\item[VLinux Bioinformatics Workbench]
+
+ Also \printurl{bioinformatics.org/vlinux}{VLinux} is at the time of
+ writing a Live CD based on the same outdated Knoppix version 3.3 as
+ Vigyann and includes a slightly changed software selection and
+ surely a different background layout.
+
+\end{description}
+
+These are too many different initiatives that could all well do much more
+in order to share the burden of maintenance and updates. With Debian
+they have he right basic infrastructure. The time will show, whose packages
+will gain most momentum.
+
+
+\subsection{Bioinformatics and Debian-Med}
+
+Debian-Med is a Custom Debian Distribution with the aim to develop
+Debian into an operating system that is particularly well fit for the
+requirements for medical practice and research. The goal of Debian-Med
+is a complete system for all tasks in medical care which is build
+completely on free software.
+
+On the technical side Debian-Med contains a set of meta packages that
+declare dependencies on other Debian packages, and that way the
+complete system is prepared for solving particular tasks. A special
+user menu will be created to enhance usability for the user working in
+the field of medicine.
+
+On the organisational side the project tries to attract people working
+in the field of Free Software in medicine to share the effort of
+building a common platform which reduces the amount of work for
+developers and users. Sharing the effort in publishing free medical
+software to a large user base is a main advantage of Debian-Med.
+
+Currently inside Debian-Med applications are provided in certain
+categories: medical practice and patient management, medical research,
+hospital information systems, medical imaging, documentation,
+molecular biology and medical genetics and others. The last part
+seems to be the most interesting and will be introduced in more detail.
+
+There are two so called meta packages which are named
+\package{med-bio} and \package{med-bio-dev}. The sense of a meta
+package is that you have to install only one single package using a
+package management software inside Debian to get all interesting
+packages which are necessary for a single task. For instance if a
+user types in: \\
+\hspace*{10mm}\texttt{apt-get install med-bio} \\
+all applications inside Debian which are related to the field of
+molecular biology and medical genetics will be installed. Moreover
+system users will get an extra menu which contains all these
+applications. The \package{med-bio-dev} package just installs
+programming libraries and tools which are interesting for users who
+want to develop biological applications (for instance the NCBI
+library\cite{Wheeler2005,Jenuth2000,ncbi:2004}).
+
+The strength of Debian is the huge number of developers (more than
+1000) all over the world working in different
+fields\ref{figure:weboftrust}. Some of them are working in the field
+of biology or medicine and thus have a natural interest in developing
+a rock solid system they can relay on for their own work (not only
+commercial interest to sell service per accident). That is the reason
+why Debian is often the platform of choice for researcher in the field
+of biology: They just find what their colleagues all over the world
+are using. The more the Debian user in the field of biology report
+back about problems or wishes the more Debian maintainers are able to
+enhance their system for their own and their users profit.
+
+In order to achieve a cooperation between virtual organisations, which
+seems essential since a single Grid has many virtual organisations and
+the virtual organisations may work across Grids, an infrastructure and
+policies for their cooperation is required. We regards this as
+equivalent to the collaboration between individuals, which is exactly
+what Debian was developed for.
+
+%% Erwaehnung der wichtigsten Pakete, dann mit Referenzen
+\begin{table}
+\begin{tabular}{rp{48mm}}
+Programming libraries:& \printurl{www.bioperl.org}{BioPerl},
+ \printurl{www.biopython.org}{BioPython}\\
+Sequence similarity: & \printurl{www.ncbi.nlm.nih.gov/BLAST}{BLAST2},
+ \printurl{bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster}{Cluster3}$^*$,
+ \printurl{www.ebi.ac.uk/clustalw}{ClustalW},
+ \printurl{www.ncbi.nlm.nih.gov/sutils/e-pcr}{e-PCR}\\
+Pretty printing: & \printurl{www.ch.embnet.org/software/BOX_form.html}{Boxshade},
+ \printurl{homepages.uni-tuebingen.de/beitz/texshade.html}{TeXshade}$^*$,
+ \printurl{homepages.uni-tuebingen.de/beitz/textopo.html}{Textopo}$^*$\\
+Phylogeny: & \printurl{ftp.cse.sc.edu/bioinformatics/molphy}{Molphy},
+ \printurl{evolution.genetics.washington.edu/phylip.html}{Phylip},
+ \printurl{darwin.zoology.gla.ac.uk/~rpage/treeviewx}{Treeview} \\
+Tool collection: & \printurl{www.emboss.org}{EMBOSS}$^{**}$,
+ \printurl{emboss.sourceforge.net/apps/\#Embassy}{EMBASSY}$^{**}$,
+ \printurl{www.bioconductor.org}{Bioconductor}$^*$,
+ \printurl{www.ncbi.nlm.nih.gov/Tools}{ncbi-tools library and programs},
+ \printurl{www.arb-home.de}{ARB},
+ \printurl{frodo.wi.mit.edu/primer3/primer3_code.html}{Primer3}$^*$\\
+Molecular modeling: & \printurl{garlic.mefos.hr/garlic/index.html}{Garlic}\\
+Gene detection: & \printurl{www.tigr.org/software/glimmer}{Glimmer},
+ %GlimmerHMM$^*$,
+ \printurl{www.sanger.ac.uk/Software/Artemis}{Artemis}$^{**}$\\
+Genetics: & \printurl{www.biostat.jhsph.edu/~kbroman/qtl}{R/qtl}\\
+Viewers: & \printurl{www.umass.edu/microbio/rasmol}{Rasmol},
+ \printurl{www.hgmp.mrc.ac.uk/Registered/Option/treetool.html}{Treetool}\\
+Pattern discovery: & \printurl{www-igm.univ-mlv.fr/~marsan/smile_english.html}{SMILE}$^*$,
+ \printurl{hmmer.wustl.edu}{HMMer}\\
+\end{tabular}
+\caption{Overview on packages in Debian-Med. $^*$ marks packages of collaborators of Debian Med that are not yet part of the Debian main distribution, $^{**}$ marks Debian packages made available through third parties.}\label{table:packages}
+\end{table}
+
+Debian harbours the most known and well accepted tools in
+bioinformatics. An incomplete overview of these is given in table
+\ref{table:packages}. A more detailed overview is available at the
+\printurl{www.debian.org/devel/debian-med/microbio}{Debian-Med
+ website}. Debian has means to inform the community of programs that
+should be packed and the Debian-Med mailing list serves for an
+additional information transfer.
+
+\section{Discussion}
+
+Technically the Debian community has implemented functionalities
+for package management that
+have not been seen elsewhere. Originally motivated to achieve
+platform independence, all packages in the Debian Main distribution
+are required to be completely compilable and installable by a
+standardised set of commands. For all platforms, build daemons fully
+automated build binary packages upon the package maintainer's
+submission of a new source package. The principle to dynamically add
+all required packages (i.e. specialised libraries) and the subsequent
+removal of these packages, should be adopted by the agent and grid
+communities, fostering increased flexibility and the better
+utilisation of human and machine resources.
+
+The Debian-Med project serves as a common platform for all Free
+Software that may be utilised in medical care. Tools developed in
+computational biology is just a part of it because it is an important
+brick in medical science. With Debian-Med's
+ambition to become the platform of choice for biological work, conform
+with the principles of the
+\printurl{www.debian.org/doc/debian-policy}{Debian
+ Policy}\cite{debianpolicy}, by the means of the distribution of
+development within the Debian Society, a well established reference
+platform for bioinformatics research and its medical applications has
+evolved and will continue to improve. The organisation is open, both
+to new members and to external sites offering packages for
+installations. Initiatives for agent research and computational grids
+should strongly consider to utilise the prepared packages.
+
+From the perspective of data security for Grids or Agent Environments,
+it should be stressed that
+Debian GNU/Linux has the unique feature of the automated creation of
+\command{chroot} environments. In a dedicated directory, the minimal set of
+programs is stored to run a a Debian GNU/Linux system. A process
+started in such will not have file access to the remainder of the
+system with otherwise complete functionality. The process is
+separated, even when started as root. Hence, arbitrary packages can be
+added and computations performed, be it for the build daemon, for the
+grid or for agent environment, without accidentally or intentionally
+impeding the functioning of the underlying operating system.
+
+The concept of integrating common tools in Bioinformatics to form a
+grid is recently exploited in the
+\printurl{lattice.umiacs.umd.edu}{Lattice project} in the group of
+Michael Cummings \cite{myers:2003}. It is based on the libraries of
+the \printurl{boinc.berkeley.edu}{BOINC platform}\cite{anderson:2004},
+the successor technology of the internet-distributed search for
+extraterrestrial intelligence from Berkeley, for which libraries for
+Debian exist.
+
+\subsection{Differences from other distributions}
+
+The Debian GNU/Linux distribution differs from others in several
+ways. Firstly, Debian is a non-commercial organisation of volunteers,
+that does not sell anything. The second and most appealing difference
+is the peer review and continuous pressure among the members to
+provide a high quality of packages. The Debian society has a constitution,
+elects its leader, and transparently describes policies for the
+creation of packages utilising specific technologies.
+
+With these principles, Debian achieved the largest collection
+of ready-to-install Free Software on the Internet.
+
+
+
+\subsection{Remaining issues}
+
+Programs not submitted to the main Debian distribution, i.e. for
+the size of the binary, because of being of interest only to a very
+small user base or because of license restrictions, will require to
+be maintained externally. A Grid's VO might decide to
+create such a shared repository also for an improved accessibility
+of a repository for non-debian in-house developers, hereby improving
+the communication with the Grid's user base and its developers.
+
+
+\subsubsection{Licensing issues}
+
+Several existing programs that might be useful for specialists are not
+free in the sense of the
+\printurl{www.debian.org/social\_contract\#guidelines}{Debian Free
+ Software Guidelines} \cite{dfsg}.
+Programs that are incompatible with the
+DFSG cannot be included in the Debian main distribution.
+One famous example of this group
+is \printurl{evolution.genetics.washington.edu/phylip.html}{PhyLip}
+and the same hold for ClustalW. Both programs' licenses contain a clause
+like
+\begin{quote}
+ Permission is granted to copy and use this program provided no fee
+ is charged for it and provided that this copyright notice is not
+ removed.
+\end{quote}
+As a consequence no reseller of Debian would be allowed to sell Debian
+because one CD contains PhyLip.
+Hence, this program may not be redistributed per default with the main
+and essential tools of Debian. Problems are, starting with those for the user:
+\begin{itemize}
+\item Need to obtain PhyLip from a different source
+\item If the user is not using a "common" architecture like {\ttfamily
+ i386} he might run into problems in compiling the latest version
+ as only the packages of the main distribution are submitted to the build daemons to save resources.
+%\item No extra security checks from his trusted operating system vendor.
+\item The user might not even notice that something like PhyLip exists
+ at all. Debian-Med cares for pointing users to relevant software
+ and thus the user will be pointed to each single program package
+ {\itshape inside\/} Debian which of interest for biological
+ research.
+\end{itemize}
+
+%While Debian Med supperts packages in the non-free section of
+%Debian this might be dropped at any time and has certain constraints.
+From the developers point of view we face also drawbacks:
+\begin{itemize}
+\item Possibly smaller user base (see last point above)
+\item Fewer bug reports and thus lower chance to increase the quality
+ of their software.
+\item \halfsloppy Porting problems to different architectures might
+ not be revealed early.
+\end{itemize}
+
+While every author is perfectly free to choose this kind of license,
+Free Software experts agree that this kind of restrictions is
+possibly a drawback for those programs because they do not fully use
+the spinning power of Free Software development.
+
+
+\subsubsection{Importance of community support}
+
+That strong support within the community of users is essential for the
+development of software, for quality assurance, feedback on features,
+and not at least for the motivation of staff, all commercial
+distributors are well aware of. E.g., RedHat has initiated Fedora as
+a free supplement to their commercial distribution. It is this reason
+why Debian-Med is part of Debian and why groups external to the Debian
+society, like BioLinux, are also keen on close collaborations with the
+community.
+
+
+\subsubsection{Road map to come closer to Debian-Med}
+
+\begin{enumerate}
+\item Join the \printurl{lists.debian.org/debian-med}{Debian-Med
+ mailing list}.
+\item Check what projects are missing and ask Debian maintainers for
+ official inclusion. There is a sponsoring program by which even non
+ Debian developers can provide packages which are checked and
+ uploaded by official maintainers. There is no point in keeping good
+ quality softwares outside of Debian.
+\item \halfsloppy Verify whether one needs special configuration for
+ your project. If yes, verify which possibilities are given in the
+ Custom Debian Distribution effort. It is more than collecting
+ software but bringing the software to your target users while taking
+ the burden from any configuration issues from his back.
+\item The only reason to keep things outside of Debian are licenses
+ which are not compatible with DFSG. All other parts of your
+ projects can be included and your time for everyday package building
+ tasks can be saved and the workload shared with other people
+ following the same road.
+\end{enumerate}
+
+There are two ways to obtain Debian GNU/Linux:
+\begin{enumerate}
+\item Installation from a CD that may be borrowed from a friend, or
+ bought from a commercial vendor. This may be together with a
+ computer magazine on a newsstand or from a redistributor on the
+ Internet.
+\item Download Debian from the web for free from a local mirror.
+\end{enumerate}
+
+The latter is the common way, a net install will only download the
+required packages.
+
+
+\subsubsection{Biological databases}
+
+The Debian community has yet not addressed the problem of
+incorporating biological databases into Debian. It seems not likely
+that this will happen in the Debian main distribution. The extra
+burden to maintain copies of e.g. the EMBL DNA sequence database on
+multiple mirrors of Debian puts too much of a burden to the mirrors
+with only little gain. And not everybody requires regular updates
+with the associated network traffic and the induced instability when
+exchanging the files while scripts might still be running reading the
+data. The provision of a set of tools that provides updates on demand
+seems a more likely scenario. This would then also need to manage the
+update of indices of e.g. sequence similarity tools.
+
+For now, Debian offers libraries like BioPerl with its facility to
+access online repositories, circumventing problems with the updating
+of local data. Debian is well suited though to address the issue
+because of its means of introspection, the programmer can tell which
+databases are installed and what files are available.
+
+
+\section{Conclusions}
+
+We have shown that there is a considerable heterogeneous shape of Free
+Software in biology. The continuous updates of data and the addition of
+novel important tools for a general bioinformatics environment cannot
+be performed by a single maintainer. The adherence to a policy and the
+sharing of maintenance are basic technologies to allow
+inter-institutional software projects as in computational grids and
+mobile agent technology.
+
+Debian and its special dedication to software in computational biology
+in Debian-Med, but also the technical infrastructure behind this
+community project renders a comfortable solution. The volunteers
+behind Debian-Med strive to support everybody's specific projects as
+best as they possibly can. It is the particular challenge of users of
+Free Software, to determine together with the community the available
+packages that already serve their needs or may be adapted
+respectively.
+
+For Debian to become the race-horse for agents and computational
+grids, the respective Debian packages and respective policies need to
+be created. The authors have created a Debian-based installation and
+experimental packages of the NorduGrid in Rostock. In cooperation
+with Emanuela Merelli and Ezio Bartocci from Camerino the installation
+of the BioAgents \cite{merelli:2002} environment is
+addressed under Debian. The development of a Debian package of the
+\printurl{jade.tilab.com}{JADE agent environment}\cite{Bellifemine2001}
+is currently being addressed.
+
+Explicit links between service descriptions in bioinformatics by MOBY-S
+and the Debian package management have not been implemented. Similarly, no
+efforts are known to combine it with the site selection in computational
+grids. Both seems technically feasible.
+
+Whatever choice for an infrastructure is made, with Debian it is available
+to all collaborating sites almost instantly.
+
+\subsection*{Acknowledgements}
+
+The authors thank the Debian Developers for all their work and
+particularly those who have contributed to Debian-Med and the Custom
+Debian Distributions effort. Debian is supported by donations through
+\printurl{www.spi-inc.org}{Software in the Public Interest}, a
+non-profit umbrella organisation for free software projects. Balazs
+Konya is thanked for his comments on the manuscript. This work was
+supported by the BMBF NBL3 program (FKZ 01ZZ0108) and BMBF project
+``Emerging Foodborne Pathogens in Germany'' (FKZ 01KL9901).
+Special thanks go to the Robert Koch-Institut for its supports of
+A.\~Tille and his work on Debian-Med.
Added: trunk/community/papers/05_biomed_bio/splncs.bst
===================================================================
--- trunk/community/papers/05_biomed_bio/splncs.bst (rev 0)
+++ trunk/community/papers/05_biomed_bio/splncs.bst 2010-12-03 09:41:04 UTC (rev 5530)
@@ -0,0 +1,1080 @@
+% BibTeX bibliography style `splncs'
+
+% An attempt to match the bibliography style required for use with
+% numbered references in Springer Verlag's "Lecture Notes in Computer
+% Science" series. (See Springer's documentation for llncs.sty for
+% more details of the suggested reference format.) Note that this
+% file will not work for author-year style citations.
+
+% Use \documentclass{llncs} and \bibliographystyle{splncs}, and cite
+% a reference with (e.g.) \cite{smith77} to get a "[1]" in the text.
+
+% Copyright (C) 1999 Jason Noble.
+% Last updated: Thursday 20 May 1999, 13:22:19
+%
+% Based on the BibTeX standard bibliography style `unsrt'
+
+ENTRY
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+ author
+ booktitle
+ chapter
+ edition
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+ pages
+ publisher
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+ if$
+}
+
+FUNCTION {not}
+{ { #0 }
+ { #1 }
+ if$
+}
+
+FUNCTION {and}
+{ 'skip$
+ { pop$ #0 }
+ if$
+}
+
+FUNCTION {or}
+{ { pop$ #1 }
+ 'skip$
+ if$
+}
+
+FUNCTION {new.block.checka}
+{ empty$
+ 'skip$
+ 'new.block
+ if$
+}
+
+FUNCTION {new.block.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.block
+ if$
+}
+
+FUNCTION {new.sentence.checka}
+{ empty$
+ 'skip$
+ 'new.sentence
+ if$
+}
+
+FUNCTION {new.sentence.checkb}
+{ empty$
+ swap$ empty$
+ and
+ 'skip$
+ 'new.sentence
+ if$
+}
+
+FUNCTION {field.or.null}
+{ duplicate$ empty$
+ { pop$ "" }
+ 'skip$
+ if$
+}
+
+FUNCTION {emphasize}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "" swap$ * "" * }
+ if$
+}
+
+FUNCTION {bold}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "\textbf{" swap$ * "}" * }
+ if$
+}
+
+FUNCTION {parens}
+{ duplicate$ empty$
+ { pop$ "" }
+ { "(" swap$ * ")" * }
+ if$
+}
+
+INTEGERS { nameptr namesleft numnames }
+
+FUNCTION {format.springer.names}
+{ 's :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr "{vv~}{ll}{, jj}{, f{.}.}" format.name$ 't :=
+ nameptr #1 >
+ { namesleft #1 >
+ { ", " * t * }
+ { numnames #1 >
+ { ", " * }
+ 'skip$
+ if$
+ t "others" =
+ { " et~al." * }
+ { "" * t * }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {format.names}
+{ 's :=
+ #1 'nameptr :=
+ s num.names$ 'numnames :=
+ numnames 'namesleft :=
+ { namesleft #0 > }
+ { s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't :=
+ nameptr #1 >
+ { namesleft #1 >
+ { ", " * t * }
+ { numnames #2 >
+ { "," * }
+ 'skip$
+ if$
+ t "others" =
+ { " et~al." * }
+ { " \& " * t * }
+ if$
+ }
+ if$
+ }
+ 't
+ if$
+ nameptr #1 + 'nameptr :=
+ namesleft #1 - 'namesleft :=
+ }
+ while$
+}
+
+FUNCTION {format.authors}
+{ author empty$
+ { "" }
+ { author format.springer.names }
+ if$
+}
+
+FUNCTION {format.editors}
+{ editor empty$
+ { "" }
+ { editor format.springer.names
+ editor num.names$ #1 >
+ { ", eds." * }
+ { ", ed." * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.title}
+{ title empty$
+ { "" }
+ { title "t" change.case$ }
+ if$
+}
+
+FUNCTION {n.dashify}
+{ 't :=
+ ""
+ { t empty$ not }
+ { t #1 #1 substring$ "-" =
+ { t #1 #2 substring$ "--" = not
+ { "--" *
+ t #2 global.max$ substring$ 't :=
+ }
+ { { t #1 #1 substring$ "-" = }
+ { "-" *
+ t #2 global.max$ substring$ 't :=
+ }
+ while$
+ }
+ if$
+ }
+ { t #1 #1 substring$ *
+ t #2 global.max$ substring$ 't :=
+ }
+ if$
+ }
+ while$
+}
+
+FUNCTION {format.date}
+{ year empty$
+ { "there's no year in " cite$ * warning$ }
+ 'year
+ if$
+}
+
+FUNCTION {format.btitle}
+{ title emphasize
+}
+
+FUNCTION {tie.or.space.connect}
+{ duplicate$ text.length$ #3 <
+ { "~" }
+ { " " }
+ if$
+ swap$ * *
+}
+
+FUNCTION {either.or.check}
+{ empty$
+ 'pop$
+ { "can't use both " swap$ * " fields in " * cite$ * warning$ }
+ if$
+}
+
+FUNCTION {format.bvolume}
+{ volume empty$
+ { "" }
+ { "Volume" volume tie.or.space.connect
+ series empty$
+ 'skip$
+ { " of " * series emphasize * }
+ if$
+ add.period$
+ "volume and number" number either.or.check
+ }
+ if$
+}
+
+FUNCTION {format.number.series}
+{ volume empty$
+ { number empty$
+ { series field.or.null }
+ { output.state mid.sentence =
+ { "number" }
+ { "Number" }
+ if$
+ number tie.or.space.connect
+ series empty$
+ { "there's a number but no series in " cite$ * warning$ }
+ { " in " * series * }
+ if$
+ }
+ if$
+ }
+ { "" }
+ if$
+}
+
+FUNCTION {format.edition}
+{ edition empty$
+ { "" }
+ { output.state mid.sentence =
+ { edition "l" change.case$ " edn." * }
+ { edition "t" change.case$ " edn." * }
+ if$
+ }
+ if$
+}
+
+INTEGERS { multiresult }
+
+FUNCTION {multi.page.check}
+{ 't :=
+ #0 'multiresult :=
+ { multiresult not
+ t empty$ not
+ and
+ }
+ { t #1 #1 substring$
+ duplicate$ "-" =
+ swap$ duplicate$ "," =
+ swap$ "+" =
+ or or
+ { #1 'multiresult := }
+ { t #2 global.max$ substring$ 't := }
+ if$
+ }
+ while$
+ multiresult
+}
+
+FUNCTION {format.pages}
+{ pages empty$
+ { "" }
+ { pages multi.page.check
+ { "" pages n.dashify tie.or.space.connect }
+ { "" pages tie.or.space.connect }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.vol}
+{ volume bold
+}
+
+FUNCTION {pre.format.pages}
+{ pages empty$
+ 'skip$
+ { duplicate$ empty$
+ { pop$ format.pages }
+ { " " * pages n.dashify * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.chapter.pages}
+{ chapter empty$
+ 'format.pages
+ { type empty$
+ { "chapter" }
+ { type "l" change.case$ }
+ if$
+ chapter tie.or.space.connect
+ pages empty$
+ 'skip$
+ { " " * format.pages * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.in.ed.booktitle}
+{ booktitle empty$
+ { "" }
+ { editor empty$
+ { "In: " booktitle emphasize * }
+ { "In " format.editors * ": " * booktitle emphasize * }
+ if$
+ }
+ if$
+}
+
+FUNCTION {empty.misc.check}
+{ author empty$ title empty$ howpublished empty$
+ month empty$ year empty$ note empty$
+ and and and and and
+ { "all relevant fields are empty in " cite$ * warning$ }
+ 'skip$
+ if$
+}
+
+FUNCTION {format.thesis.type}
+{ type empty$
+ 'skip$
+ { pop$
+ type "t" change.case$
+ }
+ if$
+}
+
+FUNCTION {format.tr.number}
+{ type empty$
+ { "Technical Report" }
+ 'type
+ if$
+ number empty$
+ { "t" change.case$ }
+ { number tie.or.space.connect }
+ if$
+}
+
+FUNCTION {format.article.crossref}
+{ key empty$
+ { journal empty$
+ { "need key or journal for " cite$ * " to crossref " * crossref *
+ warning$
+ ""
+ }
+ { "In {\em " journal * "\/}" * }
+ if$
+ }
+ { "In " key * }
+ if$
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.crossref.editor}
+{ editor #1 "{vv~}{ll}" format.name$
+ editor num.names$ duplicate$
+ #2 >
+ { pop$ " et~al." * }
+ { #2 <
+ 'skip$
+ { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
+ { " et~al." * }
+ { " and " * editor #2 "{vv~}{ll}" format.name$ * }
+ if$
+ }
+ if$
+ }
+ if$
+}
+
+FUNCTION {format.book.crossref}
+{ volume empty$
+ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
+ "In "
+ }
+ { "Volume" volume tie.or.space.connect
+ " of " *
+ }
+ if$
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {format.incoll.inproc.crossref}
+{ editor empty$
+ editor field.or.null author field.or.null =
+ or
+ { key empty$
+ { booktitle empty$
+ { "need editor, key, or booktitle for " cite$ * " to crossref " *
+ crossref * warning$
+ ""
+ }
+ { "" }
+ if$
+ }
+ { "" }
+ if$
+ }
+ { "" }
+ if$
+ " \cite{" * crossref * "}" *
+}
+
+FUNCTION {and.the.note}
+{ note output
+ note empty$
+ 'skip$
+ { add.period$ }
+ if$
+}
+
+FUNCTION {article}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ { journal emphasize "journal" output.check
+ format.vol output
+ format.date parens output
+ format.pages output
+ }
+ { format.article.crossref output.nonnull
+ format.pages output
+ }
+ if$
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {book}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ stupid.colon
+ format.btitle "title" output.check
+ new.sentence
+ crossref missing$
+ { format.edition output
+ format.bvolume output
+ new.block
+ format.number.series output
+ new.sentence
+ publisher "publisher" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ }
+ { format.book.crossref output.nonnull
+ }
+ if$
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {booklet}
+{ output.bibitem
+ format.authors output
+ stupid.colon
+ format.title "title" output.check
+ howpublished address new.block.checkb
+ howpublished output
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {inbook}
+{ output.bibitem
+ author empty$
+ { format.editors "author and editor" output.check }
+ { format.authors output.nonnull
+ crossref missing$
+ { "author and editor" editor either.or.check }
+ 'skip$
+ if$
+ }
+ if$
+ stupid.colon
+ crossref missing$
+ { chapter output
+ new.block
+ format.number.series output
+ new.sentence
+ "In:" output
+ format.btitle "title" output.check
+ new.sentence
+ format.edition output
+ format.bvolume output
+ publisher "publisher" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ }
+ { chapter output
+ new.block
+ format.incoll.inproc.crossref output.nonnull
+ }
+ if$
+ format.pages output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {incollection}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ new.sentence
+ format.bvolume output
+ format.number.series output
+ new.block
+ format.edition output
+ publisher "publisher" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ format.pages output
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ format.chapter.pages output
+ }
+ if$
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {inproceedings}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ new.sentence
+ format.bvolume output
+ format.number.series output
+ address empty$
+ { organization publisher new.sentence.checkb
+ organization empty$
+ 'skip$
+ { insert.comma }
+ if$
+ organization output
+ publisher empty$
+ 'skip$
+ { insert.comma }
+ if$
+ publisher output
+ format.date parens output
+ }
+ { insert.comma
+ address output.nonnull
+ organization empty$
+ 'skip$
+ { insert.comma }
+ if$
+ organization output
+ publisher empty$
+ 'skip$
+ { insert.comma }
+ if$
+ publisher output
+ format.date parens output
+ }
+ if$
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ }
+ if$
+ format.pages output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {conference} { inproceedings }
+
+FUNCTION {manual}
+{ output.bibitem
+ author empty$
+ { organization empty$
+ 'skip$
+ { organization output.nonnull
+ address output
+ }
+ if$
+ }
+ { format.authors output.nonnull }
+ if$
+ stupid.colon
+ format.btitle "title" output.check
+ author empty$
+ { organization empty$
+ { address new.block.checka
+ address output
+ }
+ 'skip$
+ if$
+ }
+ { organization address new.block.checkb
+ organization output
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ }
+ if$
+ new.sentence
+ format.edition output
+ format.date parens output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {mastersthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ "Master's thesis" format.thesis.type output.nonnull
+ school empty$
+ 'skip$
+ { insert.comma }
+ if$
+ school "school" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {misc}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ howpublished new.block.checka
+ howpublished output
+ format.date parens output
+ and.the.note
+ fin.entry
+ empty.misc.check
+}
+
+FUNCTION {phdthesis}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.btitle "title" output.check
+ new.block
+ "PhD thesis" format.thesis.type output.nonnull
+ school empty$
+ 'skip$
+ { insert.comma }
+ if$
+ school "school" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {proceedings}
+{ output.bibitem
+ editor empty$
+ { organization empty$
+ { "" }
+ { organization output
+ stupid.colon }
+ if$
+ }
+ { format.editors output.nonnull
+ stupid.colon
+ }
+ if$
+ format.btitle "title" output.check
+ new.block
+ crossref missing$
+ { format.in.ed.booktitle "booktitle" output.check
+ new.sentence
+ format.bvolume output
+ format.number.series output
+ address empty$
+ { organization publisher new.sentence.checkb
+ organization empty$
+ 'skip$
+ { insert.comma }
+ if$
+ organization output
+ publisher empty$
+ 'skip$
+ { insert.comma }
+ if$
+ publisher output
+ format.date parens output
+ }
+ { insert.comma
+ address output.nonnull
+ organization empty$
+ 'skip$
+ { insert.comma }
+ if$
+ organization output
+ publisher empty$
+ 'skip$
+ { insert.comma }
+ if$
+ publisher output
+ format.date parens output
+ }
+ if$
+ }
+ { format.incoll.inproc.crossref output.nonnull
+ }
+ if$
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {techreport}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ format.tr.number output.nonnull
+ institution empty$
+ 'skip$
+ { insert.comma }
+ if$
+ institution "institution" output.check
+ address empty$
+ 'skip$
+ { insert.comma }
+ if$
+ address output
+ format.date parens output
+ and.the.note
+ fin.entry
+}
+
+FUNCTION {unpublished}
+{ output.bibitem
+ format.authors "author" output.check
+ stupid.colon
+ format.title "title" output.check
+ new.block
+ note "note" output.check
+ format.date parens output
+ fin.entry
+}
+
+FUNCTION {default.type} { misc }
+
+MACRO {jan} {"January"}
+
+MACRO {feb} {"February"}
+
+MACRO {mar} {"March"}
+
+MACRO {apr} {"April"}
+
+MACRO {may} {"May"}
+
+MACRO {jun} {"June"}
+
+MACRO {jul} {"July"}
+
+MACRO {aug} {"August"}
+
+MACRO {sep} {"September"}
+
+MACRO {oct} {"October"}
+
+MACRO {nov} {"November"}
+
+MACRO {dec} {"December"}
+
+MACRO {acmcs} {"ACM Computing Surveys"}
+
+MACRO {acta} {"Acta Informatica"}
+
+MACRO {cacm} {"Communications of the ACM"}
+
+MACRO {ibmjrd} {"IBM Journal of Research and Development"}
+
+MACRO {ibmsj} {"IBM Systems Journal"}
+
+MACRO {ieeese} {"IEEE Transactions on Software Engineering"}
+
+MACRO {ieeetc} {"IEEE Transactions on Computers"}
+
+MACRO {ieeetcad}
+ {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}
+
+MACRO {ipl} {"Information Processing Letters"}
+
+MACRO {jacm} {"Journal of the ACM"}
+
+MACRO {jcss} {"Journal of Computer and System Sciences"}
+
+MACRO {scp} {"Science of Computer Programming"}
+
+MACRO {sicomp} {"SIAM Journal on Computing"}
+
+MACRO {tocs} {"ACM Transactions on Computer Systems"}
+
+MACRO {tods} {"ACM Transactions on Database Systems"}
+
+MACRO {tog} {"ACM Transactions on Graphics"}
+
+MACRO {toms} {"ACM Transactions on Mathematical Software"}
+
+MACRO {toois} {"ACM Transactions on Office Information Systems"}
+
+MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}
+
+MACRO {tcs} {"Theoretical Computer Science"}
+
+READ
+
+STRINGS { longest.label }
+
+INTEGERS { number.label longest.label.width }
+
+FUNCTION {initialize.longest.label}
+{ "" 'longest.label :=
+ #1 'number.label :=
+ #0 'longest.label.width :=
+}
+
+FUNCTION {longest.label.pass}
+{ number.label int.to.str$ 'label :=
+ number.label #1 + 'number.label :=
+ label width$ longest.label.width >
+ { label 'longest.label :=
+ label width$ 'longest.label.width :=
+ }
+ 'skip$
+ if$
+}
+
+EXECUTE {initialize.longest.label}
+
+ITERATE {longest.label.pass}
+
+FUNCTION {begin.bib}
+{ preamble$ empty$
+ 'skip$
+ { preamble$ write$ newline$ }
+ if$
+ "\begin{thebibliography}{" longest.label * "}" * write$ newline$
+}
+
+EXECUTE {begin.bib}
+
+EXECUTE {init.state.consts}
+
+ITERATE {call.type$}
+
+FUNCTION {end.bib}
+{ newline$
+ "\end{thebibliography}" write$ newline$
+}
+
+EXECUTE {end.bib}
+
+
+
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