franciscozorrilla / chalmers-igem2018

COM-dFBA is a MATLAB based COMmunity Dynamic Flux Balance Analysis framework developed by the Chalmers iGEM 2018 team. For this work, we were nominated for best modeling at the Giant Jamboree.

Overview

Presented in this repository is a framework developed for community dynamic flux balance analysis simulations, COM-dFBA. This tool can be used to simulate, analyze, and visualize complex microbial communities such as the one found in the human gut. The desired community environment is simulated by generating mass balances around user-defined exchange metabolites of interest, allowing the user to design computational experiments for the analysis of competitive and cooperative interactions between organisms of interest. Additionaly, this repository includes the reconstruction script for generating a draft genome scale model for the probiotic Saccharomyces boulardii, an organism of high research interest with no high quality GEM avaialable.

Citation

This repository makes use of the RAVEN toolbox. Please follow their installation instructions if any problems arise.

Agren R et al. (2013) PLoS Comput Biol 9(3): e1002980. doi:10.1371/journal.pcbi.1002980.

Acknowledgements

We would like to thank the following people for providing guidance, feedback, and support in our modeling approach: Eduard Kerkhoven, Benjamin Sanchez, Avlant Nilsson, Jonathan Robinson, Raphael Ferreira, Boyang Ji, and Angelo Limeta. Additionally, we would like to thank everyone in the Systems & Synthetic Biology division at Chalmers, for providing us with a friendly and open work environment.

Contact Us

For support, technical issues, bug reports, etc. please contact Francisco Zorrilla.

Links

For a more detailed description of COM-dFBA please visit our Wiki page.