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Convert SimBiology(R) model to COBRA Toolbox model

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Convert SimBiology(R) model to COBRA Toolbox model

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18 Jan 2013 (Updated )

Use SimBiology for dynamic modeling and COBRA Toolbox algorithms for constraint-based modeling.

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Description

This function converts SimBiology model objects into a COBRA Toolbox model structure. It enables you to combine dynamic modeling in SimBiology with constraint-based modeling (such as FBA, OptKnock, OptGene etc.) by going back and forth between the two approaches.

As an example, imagine having a kinetic whole genome model that you combine with a bioreactor model to investigate the system dynamics. You could use this function to convert the model to a COBRA-compatible structure and find optimal knockouts to maximize some reaction. Use the result to inactivate the corresponding reaction in your kinetic model and explore the dynamic effects of such a knockout.

Some notes regarding the use of this function:
(i) It assumes that the model comes originally from a COBRA-compliant SBML file, implying that lower and upper flux bounds, flux values and objective coefficients are stored as reaction-scoped parameters with a specific name (e.g., LOWER_BOUND for the lower flux bound) and that gene-reaction maps are stored in the reaction notes using a specific format. Obviously, this model structure could also be set up directly in SimBiology without having to go through SBML.
(ii) Species and reaction IDs are lost when SBML files are imported into SimBiology. Therefore, new IDs are generated for the exported COBRA model structure.

Please refer to the function help for additional information. This function has been tested with the yeast 5 and yeast 6 models; if you encounter any bugs, please get back to me.

Required Products SimBiology
MATLAB
MATLAB release MATLAB 8.0 (R2012b)
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Updates
30 Jan 2013

Changed default Bounds behavior: When no 'Bounds' argument is given, the parameter values in the original SimBiology model will be kept. Previous behavior changed the bounds to a default value of +/- 1000

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