Multiscale Systems Biology Collaboration

Freely available software

openCOBRA toolbox

MATLAB toolbox for constraint-based reconstruction and analysis (COBRA).

LUSOL, LUMOD

Routines for dense and sparse LU factorization.

PDCO

A primal-dual interior point method for large-scale optimization with convex objective and linear constraints.

PNOPT

Proximal Newton-type methods for minimizing composite functions (unconstrained optimization of the sum of smooth and nonsmooth functions).

fastFVA

A tool to compute efficiently flux variability analysis on large-scale biochemical networks