Task: Biology Development
Description: Debian Med packages for development of micro-biology applications
 This metapackage will install Debian packages which might be helpful
 for development of applications for micro-biological research.

Depends: bioperl, bioperl-run, libncbi6-dev

Depends: mcl
X-Category: Analysis of network structure
X-Importance: Clustering of graphs

Comment: biomode is removed from Debian because it is orphaned upstream, outdated
         and doese not work with recent Emacs any more

Depends: biosquid

Depends: libvibrant6-dev
Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install
     libmotif-dev it must be possible to deinstall libvibrant6-dev without
     beeing forced to deinstall med-bio-dev as well

Depends: python-biopython
Published-Authors: P.J. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, M.J. de Hoon
Published-Title: Biopython: freely available Python tools for computational molecular biology and bioinformatics
Published-In: Bioinformatics, 25(11):1422-1423
Published-Year: 2009
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19304878

Depends: python-cogent

Depends: libbio-ruby

Depends: libbiojava-java
Published-Authors: R.C.G. Holland, T. Down, M. Pocock, A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer, M.J. Schreiber
Published-Title: BioJava: an Open-Source Framework for Bioinformatics
Published-In: Bioinformatics 24(18):2096-2097
Published-Year: 2008
Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn397
Published-DOI: 10.1093/bioinformatics/btn397

Depends: libqsearch-dev

Depends: libgenome-1.3-0-dev

Depends: libbio-mage-perl
Why: Useful for the submission of microarray data to public repositories.

Depends: libajax6-dev | libajax5-dev

Depends: libnucleus6-dev | libnucleus5-dev

Depends: libtfbs-perl

Depends: libgo-perl 

Depends: r-cran-genetics, r-cran-haplo.stats

Depends: octave-bioinfo

Depends: libbio-graphics-perl

Depends: libbio-primerdesigner-perl

Depends: libace-perl

Depends: libbiococoa-dev

Depends: libstaden-read-dev

Depends: libsrf-dev

Suggests: r-cran-rocr
Why: Even if this package is not directly connected to biology it is maintained by
     Debian Med team and should be in our focus and it is not wrong to suggest this
     package for development of biological applications based on R

Depends: seqan-dev

Depends: libbio-mage-utils-perl

Depends: libace-perl

Depends: bioconductor
Homepage: http://www.bioconductor.org/
Responsible: Debian CRAN/BioConductor/Omegahat packaging team <pkg-bioc-devel@lists.alioth.debian.org>
License: GPL/LGPL
Pkg-URL: http://wiki.debian.org/AliothPkgBioc
Pkg-Description: analysis and comprehension of genomic data
 Bioconductor is an open source and open development software project
 to provide tools for the analysis and comprehension of genomic data.
 .
 The Bioconductor core team is based primarily at the Biostatistics Unit of
 the Dana Farber Cancer Institute at the Harvard Medical School/Harvard School
 of Public Health. Other members come from various US and international
 institutions.
 .
 The broad goals of the projects are to
  * provide access to a wide range of powerful statistical and graphical methods
    for the analysis of genomic data;
  * facilitate the integration of biological metadata in the analysis of
    experimental data: e.g. literature data from PubMed, annotation data from
    LocusLink;
  * allow the rapid development of extensible, scalable, and interoperable
    software;
  * promote high-quality documentation and reproducible research;
  * provide training in computational and statistical methods for the analysis
    of genomic data.
 .
 A nice overview about all modules of BioDonductor is given at
 http://www.bioconductor.org/packages/release/bioc/

Depends: bioclipse
Homepage: http://www.bioclipse.net/
License: Eclipse Public License (EPL) + exception
Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
 The Bioclipse project is aimed at creating a Java-based, open source,
 visual platform for chemo- and bioinformatics based on the Eclipse
 Rich Client Platform (RCP). Bioclipse, as any RCP application, is based
 on a plugin architecture that inherits basic functionality and visual
 interfaces from Eclipse, such as help system, software updates,
 preferences, cross-platform deployment etc.
 .
 Bioclipse will provide functionality for chemo- and bioinformatics,
 and extension points that easily can be extended by plugins to provide
 added functionality. The first version of Bioclipse includes a
 CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin
 (bc_jmol) for 3D-visualization and a general logging plugin. To stay
 updated on upcoming features, releases, new plugins etc, please register
 for the mailing list bioclipse-announce. The development is best
 followed on the Bioclipse Wiki where we document the progress and
 ideas of the development on a daily basis.

Depends: libgff-perl
Homepage: http://www.sanger.ac.uk/Software/formats/GFF/
Responsible: David Paleino <d.paleino@gmail.com>
License: GPL-1+
WNPP: 468826
Pkg-Description: Perl bindings for GFF Annotation Protocol
 GFF (Gene Finding Feature) is a format for describing genes and other
 features associated with DNA, RNA and Protein sequences.
 .
 This package provides a Perl module to use GFF objects.

Depends: libmems-1.5-1
Homepage: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmems.html
Responsible: Andreas Tille <tille@debian.org>
License: GPL
Pkg-URL: http://people.debian.org/~tille/packages/libmems/
Pkg-Description: library to support DNA string matching and comparative genomics
 libMems is a freely available software development library to support DNA
 string matching and comparative genomics. Among other things, libMems
 implements an algorithm to perform approximate multi-MUM and multi-MEM
 identification. The algorithm uses spaced seed patterns in conjunction
 with a seed-and-extend style hashing method to identify matches. The method
 is efficient, requiring a maximum of only 16 bytes per base of the largest
 input sequence, and this data can be stored externally (i.e. on disk) to
 further reduce memory requirements.

Depends: libbio-das-perl
Homepage: http://www.biodas.org/
Responsible: Steffen Moeller <moeller@debian.org>
License: Perl Artistic License
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libbio-das-perl/trunk
Pkg-Description: interface to Distributed Annotation System (DAS)
 Bio::Das provides access to genome sequencing and annotation databases
 that export their data in Distributed Annotation System (DAS) format
 version 1.5. Both unencrypted (http:) and SSL-encrypted (https:)
 DAS servers are supported.

Depends: limma
Homepage: http://bioinf.wehi.edu.au/limma
Responsible: Steffen Moeller <moeller@debian.org>
WNPP: 293320
License: LGPL
Pkg-Description: library for linear models and differential gene expression analysis
 Limma is an essential package of the bioconductor.org effort to
 investigate gene expression data from microarrays with the
 statistical package R.

Depends: libsbml1
Homepage: http://www.sbml.org/
License: LGPL
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/libsbml/trunk/
Responsible: Moriyoshi Koizumi <mozo@sfc.keio.ac.jp>
Pkg-URL: http://www.e-cell.org/ecell/software/downloads
Pkg-Description:  System Biology Markup Language Library
 LibSBML is a library designed to help you read, write, manipulate,
 translate, and validate SBML files and data streams. It is not an
 application itself (though it does come with many example programs),
 but rather a library you can embed in your own applications.
 .
 LibSBML is written in ISO C and C++ but as a library it may be
 used from all the programming languages listed to the left. In fact,
 we strive to adhere to the natural idioms of each particular language
 to make the libSBML programming experience seamless. For example, SBML
 <listOf> elements behave like lists and sequences in Python, but
 vectors in Matlab. Also, the C and C++ interfaces are completely
 distinct (it's possible to program in pure C), but in C++ the C APIs
 may be called without sacrifcing type safety.
 .
 The LibSBML code is very portable and is supported on Linux, Windows
 (native), and Mac OS X.