GEMPro

In this repository, you will find the master GEM-PRO dataframes for (i) E. coli (iJO1366 model of metabolism) and T. maritima

GEM-PRO is a knowledge base that connects the metabolic reconstruction (i.e. all the genes and their respective gene products, the reactions they catalyze and metabolites involved in those reactions) together with protein-related data, such as experimental protein structures, complex stoichiometry, protein fold family and domain architechture

The database is highly dimensional and there is a lot of redundancy, so we have also provided 4 iPython tutorial notebooks to help users get started with how to properly use and access data found in the GEM-PRO dataframe

All ipy notebooks should be ready for use, after setting a "Rootdir" where the folder is found. All intermediate dataframes are generated in the notebooks themselves, and much of this information can also be found in the Supplementary Information (sheets in the xls files)

All information presented in this Git Repository is strictly for academic purposes and is currently under review and can be cited as: Elizabeth Brunk,Nathan Mih, Jonathan Monk, Ke Chen, Zhen Zhang, Edward J. O'Brien, Spencer Bliven, Roger L. Chang, Philip E. Bourne, Bernhard O. Palsson. Systems Biology of the Structural Proteome. (2015) unpublished