FASIMU 2.3.4 – Flux-balance Analysis based SIMUlations

FASIMU 2.3.4

:: DESCRIPTION

FASIMU (Flux-balance Analysis based SIMUlations)is a command line oriented software implementing the most frequently applied FBA(Flux-balance Analysis) algorithms. Moreover, it offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins.

::DEVELOPER

Andreas Hoppe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
CPLEX and BiNA
Java

:: DOWNLOAD

FASIMU

:: MORE INFORMATION

Citation

FASIMU: flexible software for flux-balance computation series in large metabolic networks
Andreas Hoppe , Sabrina Hoffmann , Andreas Gerasch , Christoph Gille and Hermann-Georg Holzhütter
BMC Bioinformatics 2011, 12:28

iFBA 1.0 – Integrated Flux Balance Analysis Model of Escherichia coli

iFBA 1.0

:: DESCRIPTION

iFBA (Integrated Flux Balance Analysis Model of Escherichia coli) includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches — iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) — a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations.

::DEVELOPER

Covert Systems Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
MATLAB

:: DOWNLOAD

iFBA

:: MORE INFORMATION

Citation:

Covert, M.W., Xiao, N., Chen, T.J., and Karr, J.R. (2008)
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Bioinformatics. 24(18): 2044-2050.

FBA 2.0 – Flux Balance Analysis E.coli Model

FBA 2.0

:: DESCRIPTION

FBA (flux-balance analysis) is an software used in the analysis of metabolic behavior. FBA can be used to study metabolic systems. The fundamental principle of FBA is the conservation of mass.

Another FBA website @ UCSD

::DEVELOPER

Jeremy S. Edwards & Bernhard Palsson

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

FBA

:: MORE INFORMATION

Citation:

Edwards JS, Ibarra RU, Palsson BO. (2001) Nat Biotechnol Feb;19(2):125-30 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Edwards JS, Palsson BO (2000) Proc Natl Acad Sci May 9;97(10):5528-33. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.