8519
Comment: New website
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8642
interactive tool for building, visualizing, and simulating genetic networks
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Deletions are marked like this. | Additions are marked like this. |
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||Networks||[http://labs.systemsbiology.net/bolouri/software/BioTapestry/ BioTapestry]||LGPL||depends on java||free||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 |
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 |
Interactive analysis |
GPL |
Depends on Java and JUNG |
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://biologicalnetworks.net/ ?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
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 |
Over-representation analysis |
GPL |
java plugin for [http://www.cytoscape.org/ Cytoscape] |
free |
no |
|
Over-representation analysis |
Apache |
Depends on java |
free |
no |
|
Visualisation and analysis |
Licence not found |
Depends on java |
|
no |
|
Categorization |
[http://www.c3.lanl.gov/posoc/ POSOC] |
GPL, but non-commercial => undistributable |
Depends on OpenJGraph |
licence problem |
no |
Over-represetation analysis |
not found |
Depends on POSOC |
|
no |
|
Retreival and comparison (A. Thaliana) |
[http://www.stanford.edu/~nigam/Clench/ Clench2] |
Licence not found |
Depends on perl |
|
no |
Statistical analysis |
[http://www.charite.de/ch/medgen/ontologizer/ Ontologizer] |
Licence not found |
Depends on Java |
|
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/packages/binary/ unofficial Debian/Ubuntu packages] |
free |
no |
Networks |
[http://labs.systemsbiology.net/bolouri/software/BioTapestry/ ?BioTapestry] |
LGPL |
depends on java |
free |
no |
Data mining |
[http://www.ailab.si/orange Orange] |
GPL |
Depends on Qt, Python and ?GraphViz |
free |
no |
Inferring networks |
GPL |
Depends on Java |
free |
no |
|
Alignment of networks |
GPL |
c++ program, depends on perl |
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 |
|
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 |
MIT |
|
free |
no |
|
Text mining |
BSD |
Depends on java and minorthird |
free |
no |
|
Ontology |
[http://www.biopax.org/ BioPAX] |
LGPL |
data only? |
free |
no |
Ontology editor |
[http://protege.stanford.edu/ protégé] |
MPL1.1 |
depends on java |
non-free |
no |
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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