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CoBAMP: A Python framework for metabolic pathway analysis in constraint-based models

  • Bioinformatics, No. btz598, 2019

Publisher: OUP

Abstract

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/coba ...

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