Multiscale Systems Biology Collaboration

Stanford University, UC San Diego, University of Luxembourg

Freely available software

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

CONEOPT: A primal-dual path-following method for cone programming (Matlab)

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

LUMOD: Routines for dense LU factorization and updates (f77).

LUSOL: Routines for sparse LU factorization and updates (f77, f90, and Matlab interface).

lusolZ: Matlab routines for sparse nullspace computations using SuiteSparseQR or LUSOL.

PDCO: A primal-dual interior point method for large-scale optimization with convex objective and linear constraints (Matlab).

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