Multiscale Systems Biology Collaboration

In silico models

quadLP data

MPS data files for 14 multiscale LP models used in this paper: D. Ma and M. A. Saunders, Solving multiscale linear programs using the simplex method in quadruple precision, To appear in M. Al-Baali, L. Grandinetti, and A. Purnama (eds.), Recent Developments in Numerical Analysis and Optimization, Springer Proceedings in Mathematics and Statistics.

openCOBRA toolbox

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

ME-Matrix for E. coli

minimal medium glucose, aerobic conditions, wildtype. Please cite Thiele et al., “Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage”, PLoS One, 7(9):e45635 (2012).

Thermotoga maritima

Please cite: Nogales et al., “An in silico re-design of the metabolism in Thermotoga maritima for increased biohydrogen production”, Int J Hydrogen Energ, 37(17), 12205-12218 (2012).

Synechocystis sp. PCC6803

Please cite: Nogales, J.et al., “Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.”, PNAS, 109(7):2678-83 (2012).

Bacteroides thetaiotaomicron

Please cite: Heinken et al., “Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut”, Gut Microbes, 4(1):1-13 (2013).

Mus musculus

Please cite: Heinken et al., “Systems-level characterization of the host-microbe metabolic symbiosis in the mammalian gut”, Gut Microbes, 4(1):1-13 (2013).

Human small intestinal enterocytes

Please cite: Sahoo et al., “Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells”, Human Mol Genet, 22(13):2705-2722.