Systems Biology Portalbiocyc2SBML
Convert BioCyc files into SBML
http://genome.dfci.harvard.edu/%7Ezucker/BPHYS/biocyc-open/
posted 2006.04.25
BioGrid
http://biocomp.ece.utk.edu/tools.html
posted 2006.04.25
BSTLab
The toolbox, BSTLab, implements functions common to BST-based studies and is
designed to integrate easily into the widely used Matlab environment,
automate many common tasks, and allow expansion and customization by the
user. The toolbox also includes functions needed to reformulate and
transport models from SBML, the emerging Systems Biology Markup Language.
https://bioinformatics.musc.edu/bstlab/
posted 2006.04.25
CellML2SBML
Convert CellML files into SBML
http://sbml.org/software/cellml2sbml/
posted 2006.04.25
CL-SBML
CL-SBML is a Common Lisp SBML Library
http://common-lisp.net/project/cl-sbml/
posted 2006.04.25
ecellJ
The software system ecellJ is a package for manipulating rule files for the
ecell system which is used to simulate biological reaction networks. ecellJ
was created by Jörg R. Weimar during a research stay at the Institute for Advanced
Biosciences, Keio University, Japan.
http://www.jweimar.de/ecellJ
posted 2006.04.25
KEGG2SBML
Convert KEGG files into SBML
http://www.sbml.org/kegg2sbml.html
posted 2006.04.25
libSBML
http://www.sbml.org/software/libsbml
posted 2006.04.25
MathSBML
http://www.sbml.org/mathsbml.html
posted 2006.04.25
MATLAB SBToolbox
The Systems Biology Toolbox for MATLAB offers systems biologists an open and
extensible environment, in which to explore ideas, prototype and share new
algorithms, and build applications for the analysis and simulation of
biological systems.
http://www.fcc.chalmers.se/%7Ehenning/SBtoolbox/
posted 2006.04.25
Monod
Monod -- the Modeler's Notebook and Datastore.
Monod is a web-based
environment supporting collaborative work by scientists studying complex
biological systems.
http://monod.molsci.org/
posted 2006.04.25
Pathway Tools
http://bioinformatics.ai.sri.com/ptools/
posted 2006.04.25
SBMLeditor
SBMLeditor provides the ability to use the annotation framework based on RDF
and dublin core dc:creator and dc:relation elements. Some functions provided
by libSBML are available if the library is setup properly on the system.
http://www.ebi.ac.uk/compneur-srv/SBMLeditor.html
posted 2006.04.25
SBMLR
An interface program between SBML and R. R is a free software environment
for statistical computing and graphics.
http://epbi-radivot.cwru.edu/
posted 2006.04.25
SBMLToolbox
http://sbml.org/software/sbmltoolbox
The SBMLToolbox, linking to LIBSBML, provides a set of functions that allow
an SBML model to be imported into MATLAB and stored as a structure within
the MATLAB environment.
posted 2006.04.25
SBW
posted 2006.04.25