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.
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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.
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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.
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
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
http://genomebiology.com/2009/10/6/R69
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Well, that was easier than expected. Two problems:
Well, that was easier than expected. Two problems:
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1. Before, there were only a couple subsystems. The exchange reactions as well as membrane transport reactions were classed as 'transport', so when I was restricting system input by setting the flux of all reactions in the 'Transport' subsystem to 0 I was actually preventing all membrane transport as well.  
1. Before, there were only a couple subsystems. The exchange reactions as well as membrane transport reactions were classed as 'transport', so when I was restricting system input by setting the flux of all reactions in the 'Transport' subsystem to 0 I was actually preventing all membrane transport as well.  
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2. I was allowing influx of carbon other than glucose.
2. I was allowing influx of carbon other than glucose.
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End result: After adding the subsystems, changing the script to restrict system input based on 'Exchange' rather than 'Transport', and restricting the carbon input to 10 glucose, the system correctly spit out 60 co2.
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<A HREF="http://2012.igem.org/Team:Groningen/Notebook"><FONT COLOR=#ff6700>Back to notebook</FONT></A>
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End result: After adding the subsystems, changing the script to restrict system input based on 'Exchange' rather than 'Transport', and restricting the carbon input to 10 glucose, the system correctly spit out 60 co2.
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Revision as of 16:59, 15 September 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

Well, that was easier than expected. Two problems:
1. Before, there were only a couple subsystems. The exchange reactions as well as membrane transport reactions were classed as 'transport', so when I was restricting system input by setting the flux of all reactions in the 'Transport' subsystem to 0 I was actually preventing all membrane transport as well.
2. I was allowing influx of carbon other than glucose.
End result: After adding the subsystems, changing the script to restrict system input based on 'Exchange' rather than 'Transport', and restricting the carbon input to 10 glucose, the system correctly spit out 60 co2.

Back to notebook