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Comment: biomode is removed from Debian because it is orphaned upstream, outdated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

Depends: python-biopython

Depends: python-cogent

Depends: ruby-bio

Depends: libbiojava-java

Depends: libqsearch-dev

Depends: libgenome-1.3-0-dev

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

Depends: libajax6-dev

Depends: libnucleus6-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

Depends: libzerg0-dev, libzerg-perl
Published-Title: Zerg: a very fast BLAST parser library.
Published-Authors: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
Published-In: Bioinformatics. 19(8):1035-6
Published-Year: 2003
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/12761068
Published-PubMed: 12761068

Depends: librg-reprof-bundle-perl

Depends: libsbml5-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: libchado-perl

Depends: libpal-java

Depends: libjebl2-java
Remark: Fork from jebl
 This is a branch of the original JEBL on
 http://sourceforge.net/projects/jebl/ to develop a new API and class
 library.

Depends: r-bioc-biobase
Remark: This is a part of Bioconductor project
 A nice overview about all modules of BioDonductor is given at
 http://www.bioconductor.org/packages/release/bioc/

Depends: libffindex0-dev

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: biostrings
Vcs-Git: git://git.debian.org/debian-med/r-bioc-biostrings.git
Homepage: http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html
Pkg-Description: String objects representing biological sequences, and matching algorithms
 Memory efficient string containers, string matching algorithms, and other
 utilities, for fast manipulation of large biological sequences or sets of
 sequences.

Depends: iranges
Vcs-Git: git://git.debian.org/git/debian-med/iranges.git
Homepage: http://www.bioconductor.org/packages/release/bioc/html/IRanges.html
Pkg-Description: Infrastructure for manipulating intervals on sequences
 The package provides efficient low-level and highly reusable S4 classes for
 storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
 generally, data that can be organized sequentially (formally defined as Vector
 objects), as well as views on these Vector objects.  Efficient list-like
 classes are also provided for storing big collections of instances of the basic
 classes. All classes in the package use consistent naming and share the same
 rich and consistent "Vector API" as much as possible.

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/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: pysam
Homepage: http://code.google.com/p/pysam/
Vcs-Git: git://git.debian.org/debian-med/pysam.git
Vcs-Browser: http://git.debian.org/?p=debian-med/pysam.git
Pkg-Description: interface for the SAM/BAM sequence alignment and mapping format
 Pysam is a python module for reading and manipulating Samfiles. It's a
 lightweight wrapper of the samtools C-API.
Remark: Given the large amount of code duplication (samtools, tabix), this package
 may be difficult to accept for Debian.  It is nevertheless listed here as it is a
 useable draft, hoping it may be useful to others.

Depends: libgbfp-dev
Homepage: http://code.google.com/p/gbfp/
License: GPL
Language: C
WNPP: 612814
Responsible: Scott Christley <schristley@mac.com>
Pkg-Description: GBParsy is a GenBank flatfile parser library
 GBParsy is a library of functions that parses the GenBank flatfile,
 which is a representative and popular sequence format. The library is
 optimized for speed and efficient use of memory so it can rapidly parse
 large sequence such as Arabidopsis chromosome for genomic analysis.

Depends: python-mmtk
Homepage: https://sourcesup.cru.fr/projects/mmtk/
WNPP: 657832
License: CeCILL
Language: C, Python
Pkg-Description: Python molecular modelling toolkit
 The Molecular Modelling Toolkit (MMTK) is an Open Source program library
 for molecular simulation applications.
 In addition to providing ready-to-use implementations of standard
 algorithms, MMTK serves as a code basis that can be easily extended and
 modified to deal with standard and non-standard problems in molecular
 simulations.
 .
 MMTK is a package consisting of various modules, most of them written in
 Python, and some in C.

Depends: librostlab3-dev, librostlab-doc
WNPP: 666192
License: LGPL-3+
Language: C++
Pkg-Description: C++ library from the Rost Lab
 The library provides the following facilities:
  * current working directory resource
  * exception with stack backtrace
  * file lock resource
  * passwd and group structures for C++
  * effective uid and gid resource
  * rostlab::bio::seq class with stream input operator for FASTA format
  * umask resource

Depends: librostlab-blast0-dev, librostlab-blast-doc
WNPP: 666193
License: LGPL-3+
Language: C++
Pkg-Description: very fast C++ library for parsing the output of NCBI BLAST programs
 This package provides a very fast library for parsing the default output of
 NCBI BLAST programs into a C++ structure.
 .
 libzerg is faster, but it provides only lexing (i.e. it only returns pairs
 of token identifiers and token string values).  librostlab-blast uses a
 parser generated with bison on top of a flex-generated lexer very similar to
 that of libzerg.

Depends: librg-blast-parser-perl
WNPP: 666194
License: Artistic
Language: Perl
Pkg-Description: very fast NCBI BLAST parser - binding for perl
 This package contains perl binding for a very fast C/C++ library for NCBI
 BLAST -m 0 (default) output parsing.  BLAST results are returned in a
 convenient hash structure.
