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 Custom Debian Distribution.
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 inofficial Debian package, please do not hesitate to send a description of that project to the Debian-Med mailing list
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Debian-Med packages for development of micro-biology applications
Official Debian packages
Biomode
[Biology] An Emacs mode to edit genetic data
Homepage not available
Maintainer: Mario Lang
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Version: 1.002
License: DFSG free
Official Debian package — 
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| biomode provides you several interesting commands to take
the antiparallel of a region, convert it using readseq,
runs blast on it, etc.
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Bioperl
Perl tools for computational molecular biology
http://www.bioperl.org/
Maintainer: Debian-Med Packaging Team
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Version: 1.5.2.102
License: DFSG free
Official Debian package —
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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.
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Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
http://mged.sourceforge.net/
Maintainer: Debian-Med Packaging Team
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Version: 20030502.3
License: DFSG free
Official Debian package —
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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
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Libbio-ruby
bioruby tools for computational molecular biology
Homepage not available
Maintainer: David Nusinow
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Version: 1.1.0
License: DFSG free
Official Debian package —
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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)
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Libgenome-1.3-1
toolkit for developing bioinformatic related software
http://asap.ahabs.wisc.edu/software/software-development-libraries/libgenome.html
Maintainer: Debian-Med Packaging Team
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Version: 1.3.0
License: DFSG free
Official Debian package —
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libGenome is a freely available toolkit for developing bioinformatic related
software in C++. It is intended to take the hassle out of performing common
tasks on genetic sequence and annotation data.
Among other things, libGenome can help you:
* Read and write Multi-FastA format files
* Read and write GenBank flat file database entries
* Append, chop, truncate, reverse, complement, translate, and otherwise
mangle sequence data
* Access annotation in GenBank flat files
This package contains the dynamic library.
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Mcl
the Markov Cluster algorithm
http://micans.org/mcl/
Maintainer: Philipp Benner
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Version: 1:06
License: DFSG free
Official Debian package —
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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).
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Python-biopython
Python library for bioinformatics
http://biopython.org
Maintainer: Debian-Med Packaging Team
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Version: 1.45
License: DFSG free
Official Debian package —
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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.
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R-base-core
GNU R core of statistical computing language and environment
Homepage not available
Maintainer: Dirk Eddelbuettel
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Version: 2.7.0
License: DFSG free
Official Debian package —
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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.
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Experimental or unofficial Debian packages, projects with packaging stuff in SVN
Bioconductor
analysis and comprehension of genomic data
http://www.bioconductor.org/
Responsible: Debian CRAN/BioConductor/Omegahat packaging team
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Version: N/A
License: GPL/LGPL
Unofficial Debian package
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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.
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Libbio-das-perl
interface to Distributed Annotation System (DAS)
http://www.biodas.org/
Responsible: Steffen Moeller
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Version: N/A
License: Perl Artistic License
Unofficial Debian package
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| 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.
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Libbio-mage-utils-perl — wnpp
Extra modules for classes in the MAGE package: MAGE
http://mged.sourceforge.net/
Responsible: Charles Plessy
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Version: N/A
License: MIT/X
Unofficial Debian package
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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.
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Libbiojava-java
BioJava facilitates the processing of biological data
http://www.biojava.org
Responsible: Steffen Moeller
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Version: N/A
License: LGPL
Unofficial Debian package
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| 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.
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Libgo-perl — wnpp
parses all Gene Ontology files formats and types
http://geneontology.sourceforge.net/
Responsible: Charles Plessy
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Version: N/A
License: artistic
Unofficial Debian package
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| 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.
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Libmems-1.5-1
library to support DNA string matching and comparative genomics
http://asap.ahabs.wisc.edu/software/software-development-libraries/libmems.html
Responsible: Andreas Tille
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Version: N/A
License: GPL
Unofficial Debian package
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| 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.
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Libtfbs-perl — wnpp
Perl extension for scanning a DNA sequences for TFBS
http://forkhead.cgb.ki.se/TFBS/
Responsible: Steffen Moeller
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Version: N/A
License: artistic
Unofficial Debian package
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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.
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Debian packages not available
Aceperl — wnpp
interface for the AceDB genome database system
http://stein.cshl.org/AcePerl/
Responsible: David Paleino
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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).
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Bioclipse
platform for chemo- and bioinformatics based on Eclipse
http://www.bioclipse.net/
Responsible: no one
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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.
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Libgff-perl — wnpp
Perl bindings for GFF Annotation Protocol
http://www.sanger.ac.uk/Software/formats/GFF/
Responsible: David Paleino
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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.
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Limma — wnpp
library for linear models and differential gene expression analysis
http://bioinf.wehi.edu.au/limma
Responsible: Steffen Moeller
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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.
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