Flux Coupling and the Objective Functions’ Length in EFMs
Structural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs). One useful approach is based on Linear Program (LP) techniques, which introduce an objective function to convert the...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Metabolites |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-1989/10/12/489 |
| _version_ | 1797546399904038912 |
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| author | Francisco Guil José F. Hidalgo José M. García |
| author_facet | Francisco Guil José F. Hidalgo José M. García |
| author_sort | Francisco Guil |
| collection | DOAJ |
| description | Structural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs). One useful approach is based on Linear Program (LP) techniques, which introduce an objective function to convert the stoichiometric and thermodynamic constraints into a linear program (LP), using additional constraints to generate different nontrivial modes. This work introduces FLFS-FC (Fixed Length Function Sampling with Flux Coupling), a new approach to increase the efficiency of generation of large sets of different EFMs for the network. FLFS-FC is based on the importance of the length of the objective functions used in the associated LP problem and the imposition of additional negative constraints. Our proposal overrides some of the known drawbacks associated with the EFM extraction, such as the appearance of unfeasible problems or multiple repeated solutions arising from different LP problems. |
| first_indexed | 2024-03-10T14:29:13Z |
| format | Article |
| id | doaj.art-79659b786d534cfd8b46221c1ea74d06 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T14:29:13Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-79659b786d534cfd8b46221c1ea74d062023-11-20T22:45:08ZengMDPI AGMetabolites2218-19892020-11-01101248910.3390/metabo10120489Flux Coupling and the Objective Functions’ Length in EFMsFrancisco Guil0José F. Hidalgo1José M. García2Grupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainGrupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainGrupo de Arquitectura y Computación Paralela, Universidad de Murcia, 30080 Murcia, SpainStructural analysis of constraint-based metabolic network models attempts to find the network’s properties by searching for subsets of suitable modes or Elementary Flux Modes (EFMs). One useful approach is based on Linear Program (LP) techniques, which introduce an objective function to convert the stoichiometric and thermodynamic constraints into a linear program (LP), using additional constraints to generate different nontrivial modes. This work introduces FLFS-FC (Fixed Length Function Sampling with Flux Coupling), a new approach to increase the efficiency of generation of large sets of different EFMs for the network. FLFS-FC is based on the importance of the length of the objective functions used in the associated LP problem and the imposition of additional negative constraints. Our proposal overrides some of the known drawbacks associated with the EFM extraction, such as the appearance of unfeasible problems or multiple repeated solutions arising from different LP problems.https://www.mdpi.com/2218-1989/10/12/489metabolic networkslinear programmingEFMflux modespathwayssystems biology |
| spellingShingle | Francisco Guil José F. Hidalgo José M. García Flux Coupling and the Objective Functions’ Length in EFMs Metabolites metabolic networks linear programming EFM flux modes pathways systems biology |
| title | Flux Coupling and the Objective Functions’ Length in EFMs |
| title_full | Flux Coupling and the Objective Functions’ Length in EFMs |
| title_fullStr | Flux Coupling and the Objective Functions’ Length in EFMs |
| title_full_unstemmed | Flux Coupling and the Objective Functions’ Length in EFMs |
| title_short | Flux Coupling and the Objective Functions’ Length in EFMs |
| title_sort | flux coupling and the objective functions length in efms |
| topic | metabolic networks linear programming EFM flux modes pathways systems biology |
| url | https://www.mdpi.com/2218-1989/10/12/489 |
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