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Team:Groningen/Notebook/Modeling 6June2012
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Converted SBML xml file to GDX for use in GAMS, then adapted a GAMS script to run flux balance analysis (FBA) with a CO2 objective. Unfortunately the result was a null solution. So, now the task is to reduce the involved reactions until there is a correct result, then keeping adding reactions until the solution changes. In this way I should be able to identify the problem reactions. | Converted SBML xml file to GDX for use in GAMS, then adapted a GAMS script to run flux balance analysis (FBA) with a CO2 objective. Unfortunately the result was a null solution. So, now the task is to reduce the involved reactions until there is a correct result, then keeping adding reactions until the solution changes. In this way I should be able to identify the problem reactions. | ||
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| + | Interestingly enough, the SBML model did not include subsystems for the reactions. The subsystems had to be extracted from the xls file included in the article's supplementary information. | ||
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| + | Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, and Rick L Stevens, "iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations," Genome Biology 2009, vol. 10(6) doi:10.1186/gb-2009-10-6-r69 | ||
| + | http://genomebiology.com/2009/10/6/R69 | ||
Revision as of 22:21, 6 June 2012
Converted SBML xml file to GDX for use in GAMS, then adapted a GAMS script to run flux balance analysis (FBA) with a CO2 objective. Unfortunately the result was a null solution. So, now the task is to reduce the involved reactions until there is a correct result, then keeping adding reactions until the solution changes. In this way I should be able to identify the problem reactions.
Interestingly enough, the SBML model did not include subsystems for the reactions. The subsystems had to be extracted from the xls file included in the article's supplementary information.
Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, and Rick L Stevens, "iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations," Genome Biology 2009, vol. 10(6) doi:10.1186/gb-2009-10-6-r69 http://genomebiology.com/2009/10/6/R69
