OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis
<p>Abstract</p> <p>Background</p> <p>The quantitative analysis of metabolic fluxes, i.e., <it>in vivo </it>activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is ba...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-05-01
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| Series: | Microbial Cell Factories |
| Online Access: | http://www.microbialcellfactories.com/content/8/1/25 |
| _version_ | 1828765930775117824 |
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| author | Nielsen Lars K Wittmann Christoph Quek Lake-Ee Krömer Jens O |
| author_facet | Nielsen Lars K Wittmann Christoph Quek Lake-Ee Krömer Jens O |
| author_sort | Nielsen Lars K |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The quantitative analysis of metabolic fluxes, i.e., <it>in vivo </it>activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on <sup>13</sup>C substrates, (ii) <sup>13</sup>C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis.</p> <p>Results</p> <p>We have developed OpenFLUX as a user friendly, yet flexible software application for small and large scale <sup>13</sup>C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU) framework, significantly enhancing computation speed for flux calculation. From simple notation of metabolic reaction networks defined in a spreadsheet, the OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer balances, thus strongly facilitating model creation. The model can be used to perform experimental design, parameter estimation and sensitivity analysis either using the built-in <it>gradient-based search </it>or <it>Monte Carlo </it>algorithms or in user-defined algorithms. Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an Excel file containing metabolic reactions and carbon transfer mechanisms, showing it's user-friendliness. It reliably reproduced the published data and optimum flux distributions for the network under study were found quickly (<20 sec).</p> <p>Conclusion</p> <p>We have developed a fast, accurate application to perform steady-state <sup>13</sup>C metabolic flux analysis. OpenFLUX will strongly facilitate and enhance the design, calculation and interpretation of metabolic flux studies. By providing the software <it>open source</it>, we hope it will evolve with the rapidly growing field of fluxomics.</p> |
| first_indexed | 2024-12-11T06:56:05Z |
| format | Article |
| id | doaj.art-2dfa564072804fe5b6fe0fbbcd00dba8 |
| institution | Directory Open Access Journal |
| issn | 1475-2859 |
| language | English |
| last_indexed | 2024-12-11T06:56:05Z |
| publishDate | 2009-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbial Cell Factories |
| spelling | doaj.art-2dfa564072804fe5b6fe0fbbcd00dba82022-12-22T01:16:46ZengBMCMicrobial Cell Factories1475-28592009-05-01812510.1186/1475-2859-8-25OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysisNielsen Lars KWittmann ChristophQuek Lake-EeKrömer Jens O<p>Abstract</p> <p>Background</p> <p>The quantitative analysis of metabolic fluxes, i.e., <it>in vivo </it>activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on <sup>13</sup>C substrates, (ii) <sup>13</sup>C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis.</p> <p>Results</p> <p>We have developed OpenFLUX as a user friendly, yet flexible software application for small and large scale <sup>13</sup>C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU) framework, significantly enhancing computation speed for flux calculation. From simple notation of metabolic reaction networks defined in a spreadsheet, the OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer balances, thus strongly facilitating model creation. The model can be used to perform experimental design, parameter estimation and sensitivity analysis either using the built-in <it>gradient-based search </it>or <it>Monte Carlo </it>algorithms or in user-defined algorithms. Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an Excel file containing metabolic reactions and carbon transfer mechanisms, showing it's user-friendliness. It reliably reproduced the published data and optimum flux distributions for the network under study were found quickly (<20 sec).</p> <p>Conclusion</p> <p>We have developed a fast, accurate application to perform steady-state <sup>13</sup>C metabolic flux analysis. OpenFLUX will strongly facilitate and enhance the design, calculation and interpretation of metabolic flux studies. By providing the software <it>open source</it>, we hope it will evolve with the rapidly growing field of fluxomics.</p>http://www.microbialcellfactories.com/content/8/1/25 |
| spellingShingle | Nielsen Lars K Wittmann Christoph Quek Lake-Ee Krömer Jens O OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis Microbial Cell Factories |
| title | OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis |
| title_full | OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis |
| title_fullStr | OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis |
| title_full_unstemmed | OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis |
| title_short | OpenFLUX: efficient modelling software for <sup>13</sup>C-based metabolic flux analysis |
| title_sort | openflux efficient modelling software for sup 13 sup c based metabolic flux analysis |
| url | http://www.microbialcellfactories.com/content/8/1/25 |
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