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
- 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:
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)