CoBAMP: A Python framework for metabolic pathway analysis in constraint-based models
CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involvi...
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| Formato: | article |
| Idioma: | eng |
| Publicado em: |
2019
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| Texto completo: | http://hdl.handle.net/1822/64166 |
| País: | Portugal |
| Oai: | oai:repositorium.sdum.uminho.pt:1822/64166 |
| Resumo: | CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of constraint-based models.The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp. |
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