Multiscale Systems Biology Collaboration

Stanford University, UC San Diego, University of Luxembourg

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).