The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Genome-scale model of Yarrowia lipolytica.

Diversity-based enumeration of optimal context-specific metabolic networks

IgemRNA is an open access toolbox for transcriptome data statistical and biochemical network topology-based analysis. IgemRNA was developed in the MATLAB environment in order to take advantage of the up-to-date and most commonly distributed GSM modelling tool Cobra Toolbox 3.0 and spreadsheet file capabilities.

TBN_learning is a MATLAB implemented hybrid algorithm for learning the structure of transcriptional Bayesian networks on a genome-wide scale.