FASIMU: Flux-balance Analysis based SIMUlations


BiNA Visualization

Computed flux distributions can be graphically analyzed in BiNA in conjunction with the faBiNA plugin. It is recommended to download BiNA with the faBiNA preinstalled

Cytoscape Visualization

Computed flux distributions can be graphically analyzed in Cytoscape with the plugin FluxViz which can be downloaded from SourceForge page of FluxViz. It can also be obtained from the internal plugin structure of cytoscape.


FASIMU can neatly work together with the CellNetAnalyzer. It uses the same internal data format, so the metabolic model which is analyzed with in CellNetAnalyzer can be put directly in FASIMU, and the flux distributions computed (prepared with allout2valfiles) can be read in with the "Load scenario function" in CellNetAnalyzer.


FASIMU makes use of a lot of the goodies offered by the commercial solver IBM ILOG CPLEX and is therfore recommended. See also this Wikipedia article.

FASIMU can alternatively use the free solver lp_solve. There is a blog group on this solver and a documentation page.

FASIMU can also use the free solver GLPK documented in this Wikepedia article available from the GLPK SourceForge project.

FASIMU can also use the commercial solver LINDO API offered from LINDO Systems Inc..


If you found a bug in FASIMU, please submit it to the Bug tracking.

You may discuss FASIMU in the forum.

Here is the public task manager.

There is a survey site on FASIMU.

Main project page on bioinformatics.org.