Systems Biology Software

  • BioNetGen 2.1.5
  • Cain 1.5
  • CellDesigner 4.1 (including plugin SBMLsqueezer 1.3)
  • COPASI 4.5.30 with java and python bindings
  • Cytoscape 2.8.1 (including plugin BiNoM 1)
  • Edinburgh Pathway Editor 3.0.0
  • Ekee 2.0.2
  • ISATools 1.3
  • JSim 1.6.98
  • libSBML 3.4.1 (with java, python, matlab bindings)
  • libSBML 4.1.0 (with java, python, matlab bindings, in /opt/lib/)
  • modelMage 1.0beta
  • OpenAlea/VPlants/Alinea 0.9
  • Protege 4.1-beta.213
  • RuleBuilder 1.51
  • SBML2LaTeX 0.9.8
  • SBML-PET-MPI 1.1 (also in a singlecore version)
  • SBMLeditor 1.3.4
  • SystemsBiologyWorkbench 2.8.1
  • SQuad 2
  • semanticSBML 1.0.11
  • STSE 20110222svn
  • Taverna Workbench 2.2.0
  • vanted 1.9
  • vcell 4.8beta
  • vmd 1.8.7
  • TiDE 1.2.1
  • Xppaut 6.0

Systems Biology Models

  • BioModels Database 27.04.10
  • Yeast consensus model version 2.0

Convenience Tools

  • gtk-recordMyDesktop
  • TexLive 2009
  • QTOctave 0.9.2 with many octave-modules
  • XML Copy Editor 1.2.0.6

Python

  • BooleanNet 1.2.5
  • epydoc 3.0.1
  • NumArray 1.5.2
  • NumPy 1.3.1
  • PysCes 0.7.8
  • Python 2.6.6
  • IPython 0.10
  • PyX 0.10
  • Soappy 0.12.0
  • SciPy 0.7.2
 
software_included0.5.txt · Zuletzt geändert: 2011/03/01 15:55 von ivomaintz
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