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!
Analysis of network structure
Task |
Program |
Licence |
Packaging |
Importance |
Implementation of Girvan and Newman's algorithm |
GPL |
depends on LAN/MPI and Boost |
free |
|
Implementation of Clauset et al's algorithm |
GPL |
trivial |
free |
|
Interactive analysis |
GPL |
Depends on Java and JUNG |
free |
|
Local clustering of expression vectors |
Academic |
maybe impossible because of one needs to register first |
|
|
Finding cliques in a network |
GPL |
Did not figure out if it is a library |
free |
|
Motif detection in networks |
Academic |
|
||
Calculation and visualisation of centralities |
free of charge |
java program with unclear licence |
|
|
Visualisation |
Not found |
depends on Java |
|
|
Metabolic networks |
looks complex |
free |
||
Pathway analysis |
not found |
R package |
|
|
Prediction of missing links |
GPL |
Looks easy |
|
|
Task |
Program |
Licence |
Packaging |
Importance |
Representation of networks
Program |
Licence |
Packaging |
Importance |
BSD |
packaged (main) |
|
|
GPL |
free |
||
CPLv1 |
packaged (main) |
|
|
GPL |
packaged (main) |
|
|
GPL |
packaged (graphthing) |
|
|
(L)GPL |
packaged (python-networkx) |
|
|
MIT |
packaged (python-pydot) |
|
|
GPL |
orphaned upstream since 2003 |
free |
|
LGPL |
|
free |
|
GPL |
Depends on Java |
free |
|
GPL |
Depends on java |
free |
|
GPL |
Depends on java |
free |
|
GPL |
depends on java |
free |
|
LGPL |
Depends on Java |
free |
|
LGPL |
depends on Java |
free |
|
BSD |
depends on java |
free |
|
|
depends on tulip |
|
|
Academic |
requires specific authorisation |
|
|
Program |
Licence |
Packaging |
Importance |
Things related to Gene Ontology and offspring:
Task |
Program |
Licence |
Packaging |
Importance |
Gene Ontology |
Artistic |
Some depend on perl, some on java |
free |
|
Using GO with perl |
MIT |
cpan module |
free |
|
Dataset comparison |
GPL |
free |
||
Comparison |
BSD |
depends on Java |
new |
|
Over-representation analysis |
GPL |
java plugin for Cytoscape |
free |
|
Over-representation analysis |
Apache |
Depends on java |
free |
|
Visualisation and analysis |
Licence not found |
Depends on java |
|
|
Categorization |
GPL, but non-commercial => undistributable |
Depends on OpenJGraph |
licence problem |
|
Over-represetation analysis |
not found |
Depends on POSOC |
|
|
Retreival and comparison (A. Thaliana) |
Licence not found |
Depends on perl |
|
|
Statistical analysis |
Licence not found |
Depends on Java |
|
In addition, there is a long list of tools for microarray analysis on the GO website.
Others
Task |
Program |
Licence |
Packaging |
Importance |
Networks |
LGPL |
depends on java |
free |
|
Data mining |
GPL |
Depends on Qt, Python and ?GraphViz |
free |
|
Inferring networks |
GPL |
Depends on Java |
free |
|
Alignment of networks |
GPL |
c++ program, depends on perl |
free |
|
Machine learning for data mining tasks |
GPL |
depends on java |
|
|
Multipurpose |
BSD |
not trivial? |
free |
|
Multipurpose |
BSD |
depends on java |
free |
|
Network data storage and manipulation |
Apache |
depends on Java |
free |
|
Motif analysis and visualistion |
GPL |
depends on java, based on gravisto |
free |
|
Networks |
free for academics, but strange phrasing |
java program |
|
|
Networks |
GPL |
depends on R |
free |
|
Extrapolate a network from expression and genome data |
GPL |
depends on matlab |
contrib? |
|
Inferring transcriptional module networks |
LGPL |
depends on java |
free |
|
Knowledge environment |
MIT |
|
free |
|
Text mining |
BSD |
Depends on java and minorthird |
free |
|
Ontology |
LGPL |
data only? |
free |
|
Ontology editor |
MPL1.1 |
depends on java |
non-free |
|
Task |
Program |
Licence |
Packaging |
Importance |
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