Software & Data associated with papers:

1)  K. Zhuang, G. Vemuri, R. Mahadevan. Economics of Membrane Occupancy and the Respiro-fermentation. Nature Molecular Systems Biology, 2011. COBRA Model of E. coli in MATLAB format, SBML format

2) Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments, 2011. The ISME journal.
DyMMM: Dynamic Multispecies Metabolic Modeling framework on SourceForge.

3) Yang, Laurence, William R. Cluett, and Radhakrishnan Mahadevan. EMILiO: a fast algorithm for genome-scale strain design. Metabolic engineering 13.3 (2011): 272-281. EMILiO (MATLAB) zip archive (see below)

4) F. Salimi, K. Zhuang and R. Mahadevan. Genome-scale Metabolic Modeling of a Clostridial Co-culture for Consolidated Bioprocessing, Biotechnology Journal, 2010, 5(7):726-738. Clostridium cellulolyticum and Clostridium acetobutylicum models in SBML format.

5) Yang, L., Srinivasan, S., Mahadevan. R., Cluett, W. R. Characterizing metabolic pathway diversification in the context of perturbation size. Metabolic Engineering, 2014. 28, 114-122EMILiO (MATLAB) zip archive

6) Jayasinghe, N., Mahadevan, R. Metabolic Modeling of Spatial Heterogeneity in Microbial Fuel Cells. Biotechnology Journal, 2014, 9(10), 1350-1361. MATLAB files accompanying the paper in a zip archive. (Email Dr. Mahadevan for the password)

7) Pandit, A. V., Srinivasan, S., Mahadevan, R. Redesigning metabolism based on orthogonality principles. Nature Communications, 2017, 8, 15188.