MC3: a steady-state Model and Constraint Consistency Checker for biochemical networks.
Stoichiometric models of genome-scale organisms are essential in performing steady-state analysis of cellular systems.
The code here, termed MC^3, Model and Constraint Consistency Checker, is a MATLAB based efficient computational tool.
MC^3 can be used for two purposes: (a) identifying potential connectivity and topological issues for a given stoichiometric matrix, S, and (b) flagging issues that arise during constraint-based optimization. The MC3 tool includes three distinct checking components. The first examines the results of computing the basis for the null space for S v =0; the second uses connectivity analysis; and the third utilizes Flux Variability Analysis. MC^3 takes as input a stoichiometric matrix and flux constraints, and generates a report summarizing issues.
Please reference the 2013 BMC Systems Biology paper, "MC^3: a steady-state model and constraint consistency Checker for biochemical networks", by Mona Yousofshahi, Ehsan Ullah, Russell Stern, and Soha Hassoun.