Difference between revisions of "Team:MIT/ModelingCHutch"

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We investigated three different whole-genome scale models for \textit{C. hutchinsonii} from three different online databases:
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  <li> <a href="https://www.ebi.ac.uk/biomodels-main/BMID000000140206">BioModels Database</a> </li>
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  <li> <a href="http://f-a-m-e.fame-vu.cloudlet.sara.nl/ajax/page1.php">FAME - the Flux analysis and Modeling Environment</a> </li>
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  <li> <a href="http://bioseed.mcs.anl.gov/~chenry/FIG/CGI/ModelSEEDdownload.cgi?model=Seed269798.12&file=SBML">The Model SEED</a> </li>
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These models were in SBML (Systems Biology Markup Language) format, which is a standardized XML format for representing models. The SBML models were converted into MATLAB files using the COBRA function readCbModel.m (see MATLAB script ModelImport.m). We found that the BioModels many contained gaps, repeated metabolites, or inaccurate exchange reaction bounds. We decided to use The Model SEED whole-genome scale model (Henry et al 2010) because, although it is less detailed, it contains no repeated metabolites. We modified it by fixing exchange reaction bounds, adding hypothesized reactions for lignocellulose degradation (as described below), and adding genes/reactions to account for our synthetic communication network (as described here). Since there are no reported kinetic parameters for \textit{C. hutchinsonii}, we fitted parameters to match existing data and known behavior.
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Revision as of 22:17, 18 September 2015


C. hutchinsonii Model Development
In order to implement a dFBA model for C. hutchinsonii, we obtained a valid whole-genome scale model with its central metabolism, inserted reactions for cellulose degradation into it, fitted parameters for cellulose degradation and nutrient uptake to get more realistic behavior, and ran pure culture simulations.
Obtaining a whole-genome scale metabolic model for C. hutchinsonii
We investigated three different whole-genome scale models for \textit{C. hutchinsonii} from three different online databases:
  1. BioModels Database
  2. FAME - the Flux analysis and Modeling Environment
  3. The Model SEED
These models were in SBML (Systems Biology Markup Language) format, which is a standardized XML format for representing models. The SBML models were converted into MATLAB files using the COBRA function readCbModel.m (see MATLAB script ModelImport.m). We found that the BioModels many contained gaps, repeated metabolites, or inaccurate exchange reaction bounds. We decided to use The Model SEED whole-genome scale model (Henry et al 2010) because, although it is less detailed, it contains no repeated metabolites. We modified it by fixing exchange reaction bounds, adding hypothesized reactions for lignocellulose degradation (as described below), and adding genes/reactions to account for our synthetic communication network (as described here). Since there are no reported kinetic parameters for \textit{C. hutchinsonii}, we fitted parameters to match existing data and known behavior. $$\ce{C6H5-CHO}$$
Modeling Cellulose Degradation
Parameter Fitting
dFBA Simulation of a Pure Culture of C. hutchinsonii