Difference between revisions of "Team:MIT/ModelingCHutch"
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| − | We investigated three different whole-genome scale models for | + | We investigated three different whole-genome scale models for <i>C. hutchinsonii</i> from three different online databases: |
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<li> <a href="https://www.ebi.ac.uk/biomodels-main/BMID000000140206">BioModels Database</a> </li> | <li> <a href="https://www.ebi.ac.uk/biomodels-main/BMID000000140206">BioModels Database</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 | + | 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 in DFBALab). 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 had to modify some default exchange reaction bounds and insert reactions for cellulose degradation, as described below. |
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Parameter Fitting | Parameter Fitting | ||
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| − | <div class = "text" align = " | + | |
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| + | Since there are no reported kinetic parameters for <i>C. hutchinsonii</i>, we fitted parameters to match existing data and known behavior. | ||
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dFBA Simulation of a Pure Culture of C. hutchinsonii | dFBA Simulation of a Pure Culture of C. hutchinsonii | ||
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Revision as of 22:31, 18 September 2015
Project
Dynamic Flux Balance Analysis
C. Hutchinsonii Model Development
E. Coli Model Development
Coculture Simulations and Conclusions
C. Hutchinsonii Model Development
E. Coli Model Development
Coculture Simulations and Conclusions
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 C. hutchinsonii from three different online databases:
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 in DFBALab). 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 had to modify some default exchange reaction bounds and insert reactions for cellulose degradation, as described below.
Modeling Cellulose Degradation
Parameter Fitting
Since there are no reported kinetic parameters for C. hutchinsonii, we fitted parameters to match existing data and known behavior.
dFBA Simulation of a Pure Culture of C. hutchinsonii
