6311
Comment:
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6457
Python interface to Graphviz's dot
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Deletions are marked like this. | Additions are marked like this. |
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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 |
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
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 |
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 |
|
Task |
Program |
Licence |
Packaging |
Importance |
Listed on microbio.wml? |
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