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||[http://dkbza.org/pydot.html pydot]||MIT||packaged [http://www.doc.ic.ac.uk/~pcc03/tmp/debian/ unfficial]||Very soon sponsored in Debian||no||

Short explanation:

This page lists programs which are usefull to the field of systems biology. It is mostly software to deal with graphes, networks and ontologies.

Most column names are self-explanatory. When a licence is listed as "Academic", it means that the program is only free of charge for academic, non-profit research, which makes non-compliant to the DebianFreeSoftwareGuidelines. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website.

Analysis of network structure

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Clustering of graphs

MCL

GPL

packaged ([http://packages.debian.org/mcl main])

no

Implementation of Girvan and Newman's algorithm

[http://www.cs.ucr.edu/~qyang/software.html PEBC]

GPL

depends on LAN/MPI and Boost

free

no

Implementation of Clauset et al's algorithm

[http://www.cs.unm.edu/~aaron/research/fastmodularity.htm FastCommunautyMH]

GPL

trivial

free

no

Local clustering of expression vectors

[http://research.stowers-institute.org/bioinfo/software/psi-square/index.html psi-square]

Academic

maybe impossible because of one needs to register first

no

Finding cliques in a network

[http://users.tkk.fi/~pat/cliquer.html Cliquer]

GPL

Did not figure out if it is a library

free

no

Motif detection in networks

[http://www.minet.uni-jena.de/~wernicke/motifs/ FANMOD]

Academic

depends on [http://cs.anu.edu.au/~bdm/nauty/ nauty]

no

Calculation and visualisation of centralities

[http://centibin.ipk-gatersleben.de/index.php CentiBIN]

free of charge

java program with unclear licence

no

Visualisation

[http://brak.sdsc.edu/pub/BiologicalNetworks/index.php ?BiologicalNetworks]

Not found

depends on Java

no

Metabolic networks

[http://pht.uni-koeln.de/PHT/index.html Packet Hunter Tool]

[http://pht.uni-koeln.de/PHT/cgi-bin/license.html "Similar in some aspects to GPL"]

looks complex

free

no

Pathway analysis

[http://bioinformatics.med.yale.edu/pathway-analysis/rf.htm Pathway-analysis]

not found

R package

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Representation of networks

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://www.boost.org/libs/graph/doc/index.html The Boost Graph library]

BSD

packaged ([http://packages.debian.org/unstable/source/boost main])

no

[http://www.graphviz.org/ graphviz]

CPLv1

packaged ([http://packages.debian.org/unstable/graphics/graphviz.html main)]

no

[http://www.chaosreigns.com/code/springgraph/ springgraph]

GPL

packaged ([http://packages.debian.org/unstable/graphics/springgraph main])

no

[http://graph.seul.org/ ?GraphThing]

GPL

packaged ([http://packages.debian.org/unstable/math/graphthing graphthing])

no

[https://networkx.lanl.gov/ NetworkX]

(L)GPL

depends on python, [http://bugs.debian.org/323398 ITP #323398], in [http://ftp-master.debian.org/new.html NEW]

free

no

[http://dkbza.org/pydot.html pydot]

MIT

packaged [http://www.doc.ic.ac.uk/~pcc03/tmp/debian/ unfficial]

Very soon sponsored in Debian

no

[http://atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html ?PhyloGrapher]

GPL

depends on Tcl/Tk

free

no

[http://www.gravisto.org/ gravisto]

GPL

depends on java

free

no

[http://cbi.labri.fr/eng/proviz.htm ?ProViz]

depends on tulip

no

[http://biodata.mshri.on.ca/osprey/ Osprey]

Academic

requires specific authorisation

no

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Gene Ontology

[http://geneontology.sourceforge.net/ Gene Ontlolgy]

Artistic

Some depend on perl, some on java

free

no

Using GO with perl

[http://search.cpan.org/dist/GO-TermFinder/ GO::?TermFinder]

MIT

cpan module

free

no

Dataset comparison

[http://crfb.univ-mrs.fr/GOToolBox/index.php GOToolBox]

GPL

[http://genomebiology.com/2004/5/12/R101 sources available on request]

free

no

Comparison

[http://gutsc.wustl.edu/GOurmet/ GOurmet]

BSD

depends on Java

new

no

In addition, there is a [http://www.geneontology.org/GO.tools.microarray.shtml long list of tools] for microarray analysis on the GO website.

Others

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Networks

[http://cneurocvs.rmki.kfki.hu/igraph/ The igraph library]

GPL

[http://cneurocvs.rmki.kfki.hu/igraph/debian unofficial Ubuntu packages]

free

no

Alignment of networks

[http://graemlin.stanford.edu/download.php Græmlin]

GPL

c++ program, depends on perl

free

no

Machine learning for data mining tasks

[http://www.cs.waikato.ac.nz/ml/weka/ WEKA]

GPL

depends on java

no

Multipurpose

[http://sbw.kgi.edu/research/sbwIntro.htm Systems Biology Workbench]

BSD

not trivial?

free

no

Multipurpose

[http://jung.sourceforge.net/ JUNG]

BSD

depends on java

free

no

Network data storage and manipulation

[http://www.ebi.ac.uk/intact/index.jsp ?IntAct]

Apache

depends on Java

free

no

Motif analysis and visualistion

[http://mavisto.ipk-gatersleben.de/ mavisto]

GPL

depends on java, based on gravisto

free

no

Networks

[http://angel.elte.hu/clustering/ CFinder]

free for academics, but strange phrasing

java program

no

Networks

[http://erzuli.ss.uci.edu/R.stuff/ Social Network Analysis Tools]

GPL

depends on R

free

no

Extrapolate a network from expression and genome data

[https://bioinformatics.cs.vt.edu/xcisclique/ ?XcixClique]

GPL

depends on matlab

contrib?

no

Inferring transcriptional module networks

[http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Information_Lemmens_2006/Index.html ?ReMoDiscovery]

LGPL

depends on java

free

no

Knowledge environment

[http://sourceforge.net/projects/biolingua/ ?BioBike]

MIT

free

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?


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