Multiscale Systems Biology Collaboration

In silico models

78 M models from BiGG

JSON data files for 78 Flux Balance Analysis models (LP problems) from the BiGG database. Python code to apply Double MINOS and Quad MINOS to these models is here:

83 FBA models

MPS data files for 83 Flux Balance Analysis models (LP problems) corresponding to 83 Matlab structures in a file “all_models.mat” generated by running the following notebook written by Ali Ebrahim, UC San Diego: load_models.ipynb. The MPS files were generated by these Matlab scripts: dumpMPS2.m and dumpMPS2all.m.

quadLP data

MPS data files for 14 multiscale LP models used in this paper: Solving multiscale linear programs using the simplex method in quadruple precision, pp. 223-235 in M. Al-Baali, L. Grandinetti, and A. Purnama (eds.), Numerical Analysis and Optimization, NAO-III, Muscat, Oman, January 2014, Springer Proceedings in Mathematics and Statistics, Volume 134, Springer International Publishing Switzerland 2015.

openCOBRA toolbox

COnstraints Based Reconstruction and Analysis toolbox for MATLAB.

BiGG Database, Systems Biology Research Group, University of California, San Diego

Molecular Systems Physiology Group, University of Luxembourg (Dr Ines Thiele)