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 (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks...
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| Published in | Bioinformatics (Oxford, England) Vol. 35; no. 24; pp. 5361 - 5362 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
15.12.2019
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| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1367-4811 |
| DOI | 10.1093/bioinformatics/btz598 |
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| Summary: | 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 (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs.
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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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 UID/BIO/04469/2019; NORTE-01-0145-FEDER-000004; SFRH/BD/118657/2016 USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5) |
| ISSN: | 1367-4803 1367-4811 1367-4811 |
| DOI: | 10.1093/bioinformatics/btz598 |