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

PEBC

GPL

depends on LAN/MPI and Boost

free

Implementation of Clauset et al's algorithm

FastCommunautyMH

GPL

trivial

free

Interactive analysis

Bison

GPL

Depends on Java and JUNG

free

Local clustering of expression vectors

psi-square

Academic

maybe impossible because of one needs to register first

Finding cliques in a network

Cliquer

GPL

Did not figure out if it is a library

free

Motif detection in networks

FANMOD

Academic

depends on nauty

Calculation and visualisation of centralities

CentiBIN

free of charge

java program with unclear licence

Visualisation

BiologicalNetworks

Not found

depends on Java

Metabolic networks

Packet Hunter Tool

"Similar in some aspects to GPL"

looks complex

free

Pathway analysis

Pathway-analysis

not found

R package

Prediction of missing links

Hierarchical Random Graphs

GPL

Looks easy

Task

Program

Licence

Packaging

Importance

Representation of networks

Program

Licence

Packaging

Importance

Listed on microbio.wml?

The Boost Graph library

BSD

packaged (main)

no

The igraph library

GPL

unofficial Debian binary and source packages

free

no

graphviz

CPLv1

packaged (main)

no

springgraph

GPL

packaged (main)

no

GraphThing

GPL

packaged (graphthing)

no

NetworkX

(L)GPL

packaged (python-networkx)

no

pydot

MIT

packaged (python-pydot)

no

PhyloGrapher

GPL

depends on Tcl/Tk

free

no

hypergraph

GPL

Depends on Java

free

no

Bio Layout Express 3D

GPL

Depends on java

free

no

LinLogLayout

GPL

Depends on java

free

no

gravisto

GPL

depends on java

free

no

OpenJGraph

LGPL

Depends on Java

free

no

zrgviewer

LGPL

depends on Java

free

no

prefuse

BSD

depends on java

free

no

ProViz

depends on tulip

no

Osprey

Academic

requires specific authorisation

no

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Task

Program

Licence

Packaging

Importance

Gene Ontology

Gene Ontlolgy

Artistic

Some depend on perl, some on java

free

Using GO with perl

GO::TermFinder

MIT

cpan module

free

Dataset comparison

GOToolBox

GPL

sources available on request

free

Comparison

GOurmet

BSD

depends on Java

new

Over-representation analysis

BiNGO

GPL

java plugin for Cytoscape

free

Over-representation analysis

ErmineJ

Apache

Depends on java

free

Visualisation and analysis

GOLEM

Licence not found

Depends on java

Categorization

POSOC

GPL, but non-commercial => undistributable

Depends on OpenJGraph

licence problem

Over-represetation analysis

PoGO

not found

Depends on POSOC

Retreival and comparison (A. Thaliana)

Clench2

Licence not found

Depends on perl

Statistical analysis

Ontologizer

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

Listed on microbio.wml?

Networks

BioTapestry

LGPL

depends on java

free

no

Data mining

Orange

GPL

Depends on Qt, Python and ?GraphViz

free

no

Inferring networks

LeMoNe

GPL

Depends on Java

free

no

Alignment of networks

Græmlin

GPL

c++ program, depends on perl

free

no

Machine learning for data mining tasks

WEKA

GPL

depends on java

no

Multipurpose

Systems Biology Workbench

BSD

not trivial?

free

no

Multipurpose

JUNG

BSD

depends on java

free

no

Network data storage and manipulation

IntAct

Apache

depends on Java

free

no

Motif analysis and visualistion

mavisto

GPL

depends on java, based on gravisto

free

no

Networks

CFinder

free for academics, but strange phrasing

java program

no

Networks

Social Network Analysis Tools

GPL

depends on R

free

no

Extrapolate a network from expression and genome data

XcixClique

GPL

depends on matlab

contrib?

no

Inferring transcriptional module networks

ReMoDiscovery

LGPL

depends on java

free

no

Knowledge environment

BioBike

MIT

free

no

Text mining

ghirl

BSD

Depends on java and minorthird

free

no

Ontology

BioPAX

LGPL

data only?

free

no

Ontology editor

protégé

MPL1.1

depends on java

non-free

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?


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