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

Depends: biosquid

Depends: libvibrant6-dev

Depends: python-biopython | python3-biopython

Suggests: python-biopython-sql | python3-biopython-sql, python-biopython-doc

Depends: python-cogent

Depends: ruby-bio

Depends: libbiojava-java, libbiojava3-java

Depends: libgenome-1.3-dev

Depends: libai-fann-perl

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

Depends: libnhgri-blastall-perl

Depends: libtfbs-perl

Depends: libfreecontact0-dev, libfreecontact-perl

Suggests: libfreecontact-doc

Depends: libgo-perl

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

# Depends: octave-bioinfo
# Not maintained upstream, see ROM: #620648
# Latest version: http://snapshot.debian.org/archive/debian/20100201T042505Z/pool/main/o/octave-bioinfo/octave-bioinfo_0.1.2-2.dsc

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

Depends: librg-reprof-bundle-perl

Depends: python-corepywrap, librcsb-core-wrapper0-dev

Depends: libsbml5-dev, sbmltoolbox

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.

Suggests: r-bioc-affy,
          r-bioc-affyio,
          r-bioc-altcdfenvs,
          r-bioc-annotationdbi,
          r-bioc-biocgenerics,
          r-bioc-biomart,
          r-bioc-biovizbase,
          r-bioc-bsgenome,
          r-bioc-genomeinfodb,
          r-bioc-genomicalignments,
          r-bioc-genomicfeatures,
          r-bioc-genomicranges,
          r-bioc-graph,
          r-bioc-hypergraph,
          r-bioc-iranges,
          r-bioc-makecdfenv,
          r-bioc-preprocesscore,
          r-bioc-rsamtools,
          r-bioc-shortread,
          r-bioc-snpstats,
          r-bioc-variantannotation,
          r-bioc-xvector

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: librostlab3-dev

Suggests: librostlab-doc

Depends: librostlab-blast0-dev

Suggests: librostlab-blast-doc

Depends: librg-blast-parser-perl

Depends: libsort-key-top-perl

Depends: libhmsbeagle-dev

Depends: libforester-java

X-Mark: Prospective packages are starting here.

X-Mark: Packages in Vcs - Information about these is queried from UDD as well

Depends: libbambamc-dev

Depends: libbamtools-dev

Depends: libbio-das-perl

Depends: python-mmtk
Language: C, Python

Depends: libopenms-dev

Depends: libgenometools0-dev

Depends: python-biom-format

Depends: python-rdkit

Suggests: libswarm2-dev

Depends: libgenome-perl, libgenome-model-tools-music-perl

Depends: pyfai

Depends: libhts-dev

Depends: python-htseq

Depends: python-csb | python3-csb

Depends: python-freecontact

Suggests: libgtextutils-dev

Depends: libsnp-sites1-dev

Depends: libssm-dev

Depends: librelion-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: 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: python-pysam

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: octace-bioinfo
Homepage: http://octave.sourceforge.net/bioinfo/index.html
License: GPL-2+
Pkg-Description: Bioinformatics manipulation for Octave
  aa2int:
    Convert amino acid characters into integers.
  aminolookup:
    Convert between amino acid representations.
  cleave:
    Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern.
  int2aa
    Convert amino acid integers into characters.
  seqreverse
    Reverse a nucleotide sequence.