DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis
Background: Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA). Few existing simulators address the theoretical a...
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2015
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| Online Access: | http://hdl.handle.net/1721.1/92820 https://orcid.org/0000-0001-8964-8433 https://orcid.org/0000-0003-2895-9443 https://orcid.org/0000-0002-6106-7861 |
| _version_ | 1811068574559633408 |
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| author | Gomez, Jose Alberto Hoeffner, Kai Barton, Paul I. |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Gomez, Jose Alberto Hoeffner, Kai Barton, Paul I. |
| author_sort | Gomez, Jose Alberto |
| collection | MIT |
| description | Background:
Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA). Few existing simulators address the theoretical and practical challenges of nonunique exchange fluxes or infeasible linear programs (LPs). Both are common sources of failure and inefficiencies for these simulators.
Results:
DFBAlab, a MATLAB-based simulator that uses the LP feasibility problem to obtain an extended system and lexicographic optimization to yield unique exchange fluxes, is presented. DFBAlab is able to simulate complex dynamic cultures with multiple species rapidly and reliably, including differential-algebraic equation (DAE) systems. In addition, DFBAlab's running time scales linearly with the number of species models. Three examples are presented where the performance of COBRA, DyMMM and DFBAlab are compared.
Conclusions:
Lexicographic optimization is used to determine unique exchange fluxes which are necessary for a well-defined dynamic system. DFBAlab does not fail during numerical integration due to infeasible LPs. The extended system obtained through the LP feasibility problem in DFBAlab provides a penalty function that can be used in optimization algorithms. |
| first_indexed | 2024-09-23T07:57:56Z |
| format | Article |
| id | mit-1721.1/92820 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T07:57:56Z |
| publishDate | 2015 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/928202022-09-30T01:18:55Z DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis Gomez, Jose Alberto Hoeffner, Kai Barton, Paul I. Massachusetts Institute of Technology. Department of Chemical Engineering Gomez, Jose Alberto Hoeffner, Kai Barton, Paul I. Background: Dynamic Flux Balance Analysis (DFBA) is a dynamic simulation framework for biochemical processes. DFBA can be performed using different approaches such as static optimization (SOA), dynamic optimization (DOA), and direct approaches (DA). Few existing simulators address the theoretical and practical challenges of nonunique exchange fluxes or infeasible linear programs (LPs). Both are common sources of failure and inefficiencies for these simulators. Results: DFBAlab, a MATLAB-based simulator that uses the LP feasibility problem to obtain an extended system and lexicographic optimization to yield unique exchange fluxes, is presented. DFBAlab is able to simulate complex dynamic cultures with multiple species rapidly and reliably, including differential-algebraic equation (DAE) systems. In addition, DFBAlab's running time scales linearly with the number of species models. Three examples are presented where the performance of COBRA, DyMMM and DFBAlab are compared. Conclusions: Lexicographic optimization is used to determine unique exchange fluxes which are necessary for a well-defined dynamic system. DFBAlab does not fail during numerical integration due to infeasible LPs. The extended system obtained through the LP feasibility problem in DFBAlab provides a penalty function that can be used in optimization algorithms. 2015-01-13T15:58:48Z 2015-01-13T15:58:48Z 2014-12 2014-07 2015-01-07T17:45:56Z Article http://purl.org/eprint/type/JournalArticle 1471-2105 http://hdl.handle.net/1721.1/92820 Gomez, Jose A, Kai Hoffner, and Paul I Barton. “DFBAlab: a Fast and Reliable MATLAB Code for Dynamic Flux Balance Analysis.” BMC Bioinformatics 15, no. 1 (December 2014). https://orcid.org/0000-0001-8964-8433 https://orcid.org/0000-0003-2895-9443 https://orcid.org/0000-0002-6106-7861 en http://dx.doi.org/10.1186/s12859-014-0409-8 BMC Bioinformatics Creative Commons Attribution http://creativecommons.org/licenses/by/4.0 Jose A Gomez et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Gomez, Jose Alberto Hoeffner, Kai Barton, Paul I. DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title_full | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title_fullStr | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title_full_unstemmed | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title_short | DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis |
| title_sort | dfbalab a fast and reliable matlab code for dynamic flux balance analysis |
| url | http://hdl.handle.net/1721.1/92820 https://orcid.org/0000-0001-8964-8433 https://orcid.org/0000-0003-2895-9443 https://orcid.org/0000-0002-6106-7861 |
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