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

Depends: bioperl, libncbi6-dev, mcl
Suggests: biomode, r-base-core

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

Depends: python-biopython

Depends: libbio-ruby

Depends: libqsearch-dev

Depends: libgenome-1.3-0

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

Depends: libajax5-dev, libnucleus5-dev

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.

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: aceperl
Homepage: http://stein.cshl.org/AcePerl/
Responsible: David Paleino <d.paleino@gmail.com>
License: GPL-1+ | Artistic
WNPP: 468760
Pkg-Description: interface for the AceDB genome database system
 AcePerl is an object-oriented Perl interface for the AceDB
 database. It provides functionality for connecting to remote AceDB
 databases, performing queries, fetching ACE objects, and updating
 databases. The programmer's API is compatible with the JADE Java API,
 and interoperable with the API used by BoulderIO.
 .
 AceDB is a genome database system developed since 1989 primarily by
 Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger
 Institute). It was originally developed for the C.elegans genome
 project , from which its name was derived (A C. elegans DataBase).

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
Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/libbio-das-perl/trunk/?rev=0&sc=0
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: libbiojava-java
Homepage: http://www.biojava.org
Responsible: Steffen Moeller <moeller@debian.org>
License: LGPL
Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/biojava/trunk/?rev=0&sc=0
Pkg-Description: BioJava facilitates the processing of biological data
 BioJava is an open-source project dedicated to providing a Java framework
 for processing biological data. It include objects for manipulating
 sequences, file parsers, DAS client and server support, access to BioSQL
 and Ensembl databases, and powerful analysis and statistical routines
 including a dynamic programming toolkit.

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: libtfbs-perl
Homepage: http://forkhead.cgb.ki.se/TFBS/
Responsible: Steffen Moeller <moeller@debian.org>
WNPP: 320777
License: artistic
Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/tfbs/trunk/?rev=0&sc=0
Pkg-Description: Perl extension for scanning a DNA sequences for TFBS
 TFBS Perl OO modules implement classes for the representation of objects
 encountered in analysis of protein-binding sites in DNA sequences.The
 objects defined by TFBS classes include:
  * pattern definition objects, currently position specific score matrices
    (raw frequency, information content and position weight matrices)with
    methods for interconversion between matrix types, sequence searching
    with a matrix profile, sequence 'logo' drawing and matrix manipulation;
  * a composite object representing a set of position specific score
    matrices, with methods for the identification of motifs within DNA
    sequences with the set of profiles from its member matrices;
  * methods for searching pairwise alignments for patterns conserved
    in both sequences (phylogenetic footprinting) defined for both matrix
    profile and composite (matrix set) objects;
  * an object representing DNA binding site sequence, and an object
    representing sets of DNA binding sequences, with methods and helper
    classes to facilitate scanning, filtering and statistical analyses;
  * an object representing a pair of DNA binding site sequences, and an
    object representing a set of such pairs, for storage, manipulation and
    analysis of phylogenetic footprinting searches;
  * database interfaces to relational, flat file and WWW database of
    position-specifc score matrices, with methods for searching existing
    databases, as well as creating new ones containing user-defined matrices.
  * interfaces to matrix pattern generating programs
 .
 The modules within the TFBS set are fully integrated and compatible with
 Bioperl.

Depends: libgo-perl 
Homepage: http://geneontology.sourceforge.net/
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 452923
Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/libgo-perl/trunk/?rev=0&sc=0
License: artistic
Pkg-Description: parses all Gene Ontology files formats and types
 This is a collection of perl code for dealing with Gene Ontologies (GO)
 and OBO style ontologies. It is part of the `go-dev' distribution, but
 this Debian package is made from the CPAN archive. This package
 contains both scripts (which can be used with no knowledge of perl),
 and libraries which will be of use to perl programmers using GO or OBO.

Depends: libbio-mage-utils-perl
Homepage: http://mged.sourceforge.net/
License: MIT/X
WNPP: 476202
Responsible: Charles Plessy <plessy@debian.org>
Pkg-URL: http://mentors.debian.net/debian/pool/main/l/libbio-mage-utils-perl/
Pkg-Description: Extra modules for classes in the MAGE package: MAGE
 MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the
 Microarray Gene Expression Data Society (MGED). This package contains Perl
 modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum
 Information About a Microarray Experiment) records of microarray ("DNA chips")
 experiments.
 .
 Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology,
 as well as SQL utilities.

Depends: seqan
Homepage: http://www.seqan.de/
License: LGPL
WNPP: 487361
Responsible: Soeren Sonnenburg <bugreports@nn7.de>
Pkg-Description: C++ template library for the analysis of sequences.
 SeqAn is a C++ template library of efficient algorithms and data
 structures for the analysis of sequences with the focus on
 biological data. This library applies a unique generic design that
 guarantees high performance, generality, extensibility, and
 integration with other libraries. SeqAn is easy to use and
 simplifies the development of new software tools with a minimal loss
 of performance.

