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 |
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 |
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://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://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://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? |
Things related to Gene Ontology and offspring:
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 |
Machine learning for data mining tasks |
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 |
Apache |
depends on Java |
free |
no |
|
Networks |
[https://networkx.lanl.gov/ NetworkX] |
(L)GPL |
depends on python |
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 |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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