sybil – Efficient constraint-based modelling in R

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

A MATLAB toolbox for structural kinetic modeling

(2012) D. Girbig et al.   BIOINFORMATICS

F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

(2012) Abdelhalim Larhlimi et al.   BMC BIOINFORMATICS

FASIMU: flexible software for flux-balance computation series in large metabolic networks

(2011) Andreas Hoppe et al.   BMC BIOINFORMATICS

An integrated approach to characterize genetic interaction networks in yeast metabolism

(2011) Balázs Szappanos et al.   NATURE GENETICS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

Large-scale computation of elementary flux modes with bit pattern trees

(2008) Marco Terzer et al.   BIOINFORMATICS

The Systems Biology Research Tool: evolvable open-source software

(2008) Jeremiah Wright et al.   BMC Systems Biology

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is maximization of molar yield in metabolic networks favoured by evolution?

(2007) Stefan Schuster et al.   JOURNAL OF THEORETICAL BIOLOGY