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Software

FindingMemo (2019)

Computing minimum sets of elementary flux modes in metabolic networks.

irreversibleMinimalCutSets (2019)

Computing irreversible minimal cut sets in metabolic networks.

MinimalNetwork (2017)

A mixed-integer linear programming software for computing minimal subnetworks of a genome-scale metabolic network, while preserving certain biological properties that can be specified by the user.

CEFMISTR - Computing elementary flux modes involving a set of target reactions (2013)

Elementary flux mode (EM) analysis is an important tool in the constraint-based analysis of genome-scale metabolic networks. CEFMISTR is a Matlab tool for enumerating EMs with one or two predefined reactions.

L4FC - Lattices for Flux Coupling (2013)

A smart Java 8 library to find coupled reactions in metabolic networks with Cplex.

METAOPT - Optimization toolbox for analyzing metabolic networks (2013)

Metaopt contains direct C++ implementations of metabolic analysis methods based on flux optimization. It is mainly developed to solve thermodynamically constrained FBA and FVA (tFVA) efficiently.

Fast flux coupling calculator (F2C2) (2012)

A flux coupling analysis tool, that implements the F2C2 algorithm.

FFCA: Feasibility-based Flux Coupling Analysis of metabolic networks (2011)

FFCA is a Matlab based tool for flux coupling analysis. An LP solver should be installed separately and made "visible" from within Matlab. FFCA currently supports the usage of Linprog, Clp, Lindo and Glpk.