Debian Med Project
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Summary
Biology development
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.

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Integrated Solution.

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks
Index of all tasks

Debian Med Biology development packages

Official Debian packages

Biomode
[Biology] An Emacs mode to edit genetic data
Homepage not available
Maintainer: Mario Lang
 Version: 1.002
License: DFSG free
Official Debian package -
biomode provides you several interesting commands to take the antiparallel of a region, convert it using readseq, runs blast on it, etc.
Bioperl
Perl tools for computational molecular biology 		Version: 1.5.2.102
License: DFSG free
Official Debian package -
The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl.
When publishing work prepared with this package, you should cite: J.E. Stajich, D. Block, K. Boulez, S.E. Brenner, S.A. Chervitz, C. Dagdigian, G. Fuellen, J.G. Gilbert, I. Korf, H. Lapp, H. Lehvaslaiho, C. Matsalla, C.J. Mungall, B.I. Osborne, M.R. Pocock, P. Schattner, M. Senger, L.D. Stein, E. Stupka, M.D. Wilkinson, E. Birney (2002) "The Bioperl toolkit: Perl modules for the life sciences." Genome Res. 12(10):1611-1618.
Libajax5-dev
Development files for libajax 		Version: 5.0.0
License: DFSG free
Official Debian package -
This package contains the header and development files needed to build programs and packages using libajax.
Libbio-mage-perl
Container module for classes in the MAGE package: MAGE 		Version: 20030502.3
License: DFSG free
Official Debian package -
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. 
 The Bio::MAGE module contains the following Bio::MAGE classes:
   * NameValueType
   * Extendable
   * Identifiable
   * Describable
Libbio-ruby
bioruby tools for computational molecular biology
Homepage not available
Maintainer: David Nusinow
 Version: 1.1.0
License: DFSG free
Official Debian package -
BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple and stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.
This project is a dependency package, which depends on Debian's default Ruby version (currently 1.8.x)
Libgo-perl
perl modules for GO and other OBO ontologies 		Version: 0.09
License: artistic
Official Debian package -
This is a collection of perl code for dealing with Gene Ontologies (GO) and Open Biomedical Ontologies (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.
Libncbi6-dev
NCBI libraries for biology applications (development files)
Maintainer: Aaron M. Ucko
 Version: 6.1.20080302
License: DFSG free
Official Debian package -
This package is for developers or people who want to compile programs only. In addition to development headers and libraries, it contains the utilities asntool and errhdr.
Libnucleus5-dev
Development files for libajax 		Version: 5.0.0
License: DFSG free
Official Debian package -
This package contains the header and development files needed to build programs and packages using libnucleus.
Libqsearch-dev
nondeterministic quartet tree search library for unrooted trees
Maintainer: Rudi Cilibrasi
 Version: 1.0.8
License: DFSG free
Official Debian package -
qsearch is a library for universal hierarchical clustering using an arbitrary distance matrix as input. It searches through the space of all possible unrooted trees of a given size and finds the closest match based on a weighted quartet cost function determined by the distance matrix. When used in combination with other feature extraction libraries such as libcomplearn this system can be used for fast and accurate phylogenetic reconstruction, linguistic analysis, or stemmatology.
Libtfbs-perl
scanning DNA sequence with a position weight matrix 		Version: 0.5.svn.20080722
License: artistic
Official Debian package -
The TFBS perl modules comprise a set of routines to interact with the Transfac and Jaspar databases that describe a special family of proteins, the transcription factors. These bind to genomic DNA to initiate (or prevent) the readout of a gene. Once multiple binding sites are known for a transcription factor, these are gathered in a single file and are aligned in order to find position-specific characteristica that might be used to predict such binding events in novel DNA sequences.
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
Maintainer: Aaron M. Ucko
 Version: 6.1.20080302
License: DFSG free
Official Debian package -
Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications.
Mcl
the Markov Cluster algorithm
Maintainer: Philipp Benner
 Version: 1:06
License: DFSG free
Official Debian package -
The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments.
MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis).
Python-biopython
Python library for bioinformatics 		Version: 1.47
License: DFSG free
Official Debian package -
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project.
R-base-core
GNU R core of statistical computing language and environment
Maintainer: Dirk Eddelbuettel
 Version: 2.7.2
License: DFSG free
Official Debian package -
R is `GNU S' - A language and environment for statistical computing and graphics. R is similar to the award-winning S system, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).
R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, C, C++ and Fortran code can be linked and called at run time.
S is the statistician's Matlab and R is to S what Octave is to Matlab.
This package provides the core GNU R system from which only the optional documentation packages r-base-html, r-base-latex, r-doc-html, r-doc-pdf and r-doc-info have been split off to somewhat reduce the size of this package.
R-cran-genetics
GNU R package for population genetics
Maintainer: Steffen Moeller
 Version: 1.3.3
License: GPL
Official Debian package -
Classes and methods for handling genetic data. Includes The package provides a library for the statistics environment R that contains classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, and more.
R-cran-haplo.stats
GNU R package for haplotype analysis
Maintainer: Steffen Moeller
 Version: 1.3.8
License: GPL
Official Debian package -
The package provides routines for the GNU R statistics environment for statistical Analysis of indirectly measured Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap.

Experimental or unofficial Debian packages, projects with packaging stuff in SVN

Bioconductor
analysis and comprehension of genomic data
License: GPL/LGPL
Unofficial Debian package
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.
Libbio-das-perl
interface to Distributed Annotation System (DAS)
Responsible: Steffen Moeller
License: Perl Artistic License
Unofficial Debian package
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.
Libbio-mage-utils-perl - wnpp
Extra modules for classes in the MAGE package: MAGE
Responsible: Charles Plessy
License: MIT/X
Unofficial Debian package
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.
Libbiojava-java
BioJava facilitates the processing of biological data
Responsible: Steffen Moeller
License: LGPL
Unofficial Debian package
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.
Libmems-1.5-1
library to support DNA string matching and comparative genomics
Responsible: Andreas Tille
License: GPL
Unofficial Debian package
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.
Libsbml1
System Biology Markup Language Library
Responsible: Moriyoshi Koizumi
License: LGPL
Unofficial Debian package
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.

Debian packages not available

Aceperl - wnpp
interface for the AceDB genome database system
Responsible: David Paleino
License: GPL-1+ | Artistic
Debian package not available
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).
Bioclipse
platform for chemo- and bioinformatics based on Eclipse
License: Eclipse Public License (EPL) + exception
Debian package not available
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.
Libgff-perl - wnpp
Perl bindings for GFF Annotation Protocol
Responsible: David Paleino
License: GPL-1+
Debian package not available
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.
Limma - wnpp
library for linear models and differential gene expression analysis
Responsible: Steffen Moeller
License: LGPL
Debian package not available
Limma is an essential package of the bioconductor.org effort to investigate gene expression data from microarrays with the statistical package R.
Seqan - wnpp
C++ template library for the analysis of sequences.
Responsible: Soeren Sonnenburg
License: LGPL
Debian package not available
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.