Summary
Biology development
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.
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 Pure Blend.
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
|
Debian Med Biology development packages
Official Debian packages
Bioperl
Perl tools for computational molecular biology
|
Version: 1.5.2.102
License: DFSG free
Official Debian package
- 
Translate description
|
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
-
Translate description
|
|
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
-
Translate description
|
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
|
Version: 1.1.0
License: DFSG free
Official Debian package
-
Translate description
|
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)
|
Libgenome-1.3-0
toolkit for developing bioinformatic related software
|
Version: 1.3.1
License: DFSG free
Official Debian package
-
Translate description
|
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.
|
Libgo-perl
perl modules for GO and other OBO ontologies
|
Version: 0.09
License: DFSG free
Official Debian package
-
Translate description
|
|
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)
|
Version: 6.1.20080302
License: DFSG free
Official Debian package
-
Translate description
|
|
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
-
Translate description
|
|
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
|
Version: 1.0.8
License: DFSG free
Official Debian package
-
Translate description
|
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: DFSG free
Official Debian package
-
Translate description
|
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.
If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002)
TFBS: Computational framework for transcription factor binding site analysis.
Bioinformatics 18:1135-1136".
|
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
|
Version: 6.1.20080302
License: DFSG free
Official Debian package
-
Translate description
|
|
Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
biological applications.
|
Mcl
the Markov Cluster algorithm
|
Version: 1:06
License: DFSG free
Official Debian package
-
Translate description
|
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).
|
Octave-bioinfo
bioinformatic functions for Octave
|
Version: 0.1.0
License: DFSG free
Official Debian package
-
Translate description
|
This package provides functions to do work in bioinformatics in
Octave, a numerical computation software. It contains functions to
convert amino acid characters into integers (aa2int), convert between
amino acid representations (aminolookup), cleave peptides (cleave),
convert integers into amino acid characters (int2aa) and reverse a
nucleotide sequence (seqreverse).
This Octave add-on package is part of the Octave-Forge project.
|
Python-biopython
Python library for bioinformatics
|
Version: 1.47
License: DFSG free
Official Debian package
-
Translate description
|
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-cran-genetics
GNU R package for population genetics
|
Version: 1.3.4
License: DFSG free
Official Debian package
-
Translate description
|
|
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
|
Version: 1.3.8
License: DFSG free
Official Debian package
-
Translate description
|
|
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.
|
Official Debian packages (Suggested)
Biomode
[Biology] An Emacs mode to edit genetic data
Homepage not available
|
Version: 1.002
License: DFSG free
Official Debian package
-
Translate description
|
|
biomode provides you several interesting commands to take
the antiparallel of a region, convert it using readseq,
runs blast on it, etc.
|
R-base-core
GNU R core of statistical computation and graphics system
|
Version: 2.8.0
License: DFSG free
Official Debian package
-
Translate description
|
R is a system for statistical computation and graphics. It consists
of a language plus a run-time environment with graphics, a debugger,
access to certain system functions, and the ability to run programs
stored in script files.
The design of R has been heavily influenced by two existing languages:
Becker, Chambers & Wilks' S and Sussman's Scheme. Whereas the
resulting language is very similar in appearance to S, the underlying
implementation and semantics are derived from Scheme.
The core of R is an interpreted computer language which allows
branching and looping as well as modular programming using functions.
Most of the user-visible functions in R are written in R. It is
possible for the user to interface to procedures written in the
C, C++, or FORTRAN languages for efficiency, and many of R's core
functions do so. The R distribution contains functionality for a
large number of statistical procedures and underlying applied math
computations. There is also a large set of functions which provide
a flexible graphical environment for creating various kinds of data
presentations.
Additionally, over thousand extension "packages" are available from
CRAN, the Comprehensive R Archive Network, many also as Debian packages,
named 'r-cran-<name>'.
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-rocr
GNU R package to prepare and display ROC curves
|
Version: 1.0
License: DFSG free
Official Debian package
-
Translate description
|
ROC graphs, sensitivity/specificity curves, lift charts,
and precision/recall plots are popular examples of trade-off
visualizations for specific pairs of performance measures. ROCR is a
flexible tool for creating cutoff-parametrized 2D performance curves
by freely combining two from over 25 performance measures (new
performance measures can be added using a standard interface).
Curves from different cross-validation or bootstrapping runs can be
averaged by different methods, and standard deviations, standard
errors or box plots can be used to visualize the variability across
the runs. The parametrization can be visualized by printing cutoff
values at the corresponding curve positions, or by coloring the
curve according to cutoff. All components of a performance plot can
be quickly adjusted using a flexible parameter dispatching
mechanism. Despite its flexibility, ROCR is easy to use, with only
three commands and reasonable default values for all optional
parameters.
ROCR features: ROC curves, precision/recall plots, lift charts, cost
curves, custom curves by freely selecting one performance measure for the
x axis and one for the y axis, handling of data from cross-validation
or bootstrapping, curve averaging (vertically, horizontally, or by
threshold), standard error bars, box plots, curves that are color-coded
by cutoff, printing threshold values on the curve, tight integration
with Rs plotting facilities (making it easy to adjust plots or to combine
multiple plots), fully customizable, easy to use (only 3 commands).
Performance measures that ROCR knows: Accuracy, error rate, true
positive rate, false positive rate, true negative rate, false negative
rate, sensitivity, specificity, recall, positive predictive value,
negative predictive value, precision, fallout, miss, phi correlation
coefficient, Matthews correlation coefficient, mutual information, chi
square statistic, odds ratio, lift value, precision/recall F measure,
ROC convex hull, area under the ROC curve, precision/recall break-even
point, calibration error, mean cross-entropy, root mean squared error,
SAR measure, expected cost, explicit cost.
|
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)
|
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
|
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.
|
Libmems-1.5-1
library to support DNA string matching and comparative genomics
|
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
|
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
|
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
|
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
|
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.
|
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.
|
|
