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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Bibliographic Details
Published inBioinformatics (Oxford, England) Vol. 35; no. 24; pp. 5361 - 5362
Main Authors Vieira, Vítor, Rocha, Miguel
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.12.2019
Online AccessGet full text
ISSN1367-4803
1367-4811
1367-4811
DOI10.1093/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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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