Difference between revisions of "Team:Aachen/Modeling"
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We evaluated three candidate organisms for our conversion pathway using their genome-scale stoichiometric models: | We evaluated three candidate organisms for our conversion pathway using their genome-scale stoichiometric models: | ||
* ''Escherischia coli'' genome scale model iJO1366 <ref>http://www.jbc.org/content/239/12/4018.full.pdf</ref> | * ''Escherischia coli'' genome scale model iJO1366 <ref>http://www.jbc.org/content/239/12/4018.full.pdf</ref> | ||
− | * ''Saccharomyces cerevisiae'' genome scale model | + | * ''Saccharomyces cerevisiae'' genome scale model ''i''ND750 <ref>Reconstruction and validation of Saccharomyces cerevisiae ''i''ND750, a fully compartmentalized genome-scale metabolic model, Duarte et. al 2004, http://www.ncbi.nlm.nih.gov/pubmed/15197165</ref> |
* ''Pseudomonas putida'' genome scale model PpuMBEL1071 <ref>Sohn SB, Kim TY, Park JM, Lee SY. In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J. 2010 Jul;5(7):739-50. doi:10.1002/biot.201000124. PubMed PMID: 20540110.</ref> | * ''Pseudomonas putida'' genome scale model PpuMBEL1071 <ref>Sohn SB, Kim TY, Park JM, Lee SY. In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J. 2010 Jul;5(7):739-50. doi:10.1002/biot.201000124. PubMed PMID: 20540110.</ref> | ||
The models were loaded with COBRApy <ref>Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson and Daniel R Hyduke (2015) COBRApy: COnstraints-Based Reconstruction and Analysis for Python</ref> and solved with GLPK <ref>http://www.gnu.org/software/glpk/</ref>. Escher <ref>Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson (2015) Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways, PLOS Computational Biology</ref> was used for visualization. | The models were loaded with COBRApy <ref>Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson and Daniel R Hyduke (2015) COBRApy: COnstraints-Based Reconstruction and Analysis for Python</ref> and solved with GLPK <ref>http://www.gnu.org/software/glpk/</ref>. Escher <ref>Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson (2015) Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways, PLOS Computational Biology</ref> was used for visualization. | ||
− | The metabolic network is modeled under the | + | The metabolic network is modeled under the steady-state assumption, i.e., all metabolite concentrations and reaction rates are constant |
=Methanol Uptake Pathways= | =Methanol Uptake Pathways= |
Revision as of 15:28, 18 September 2015