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

Vieira, Vítor; Rocha, Miguel; Valencia, ed., Alfonso

doi:10.1093/bioinformatics/btz598

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

Abstract

Abstract 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. Availability and implementation 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.

Authors:

;

; Valencia, ed., Alfonso

Publication Date:: Mon Jul 29 00:00:00 EDT 2019

Sponsoring Org.:: USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain; USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)

OSTI Identifier:: 1582460

Alternate Identifier(s):: OSTI ID: 1563062

Grant/Contract Number:: UID/BIO/04469/2019; NORTE-01-0145-FEDER-000004; SFRH/BD/118657/2016

Resource Type:: Published Article

Journal Name:: Bioinformatics

Additional Journal Information:: Journal Name: Bioinformatics Journal Volume: 35 Journal Issue: 24; Journal ID: ISSN 1367-4803

Publisher:: Oxford University Press

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Vieira, Vítor, Rocha, Miguel, and Valencia, ed., Alfonso. CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.  United Kingdom: N. p., 2019. 
Web.  doi:10.1093/bioinformatics/btz598.

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                    Vieira, Vítor, Rocha, Miguel, & Valencia, ed., Alfonso. CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.  United Kingdom.  https://doi.org/10.1093/bioinformatics/btz598

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                    Vieira, Vítor, Rocha, Miguel, and Valencia, ed., Alfonso. Mon .  
"CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models".  United Kingdom.  https://doi.org/10.1093/bioinformatics/btz598.

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@article{osti_1582460,

  title        = {CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models},

  author       = {Vieira, Vítor and Rocha, Miguel and Valencia, ed., Alfonso},

  abstractNote = {Abstract 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. Availability and implementation 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.},

  doi          = {10.1093/bioinformatics/btz598},

  journal      = {Bioinformatics},

  number       = 24,

  volume       = 35,

  place        = {United Kingdom},

  year         = {Mon Jul 29 00:00:00 EDT 2019},

  month        = {Mon Jul 29 00:00:00 EDT 2019}

}

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Works referenced in this record:

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Similar Records

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

Abstract

Citation Formats

Computing the shortest elementary flux modes in genome-scale metabolic networks journal, September 2009

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks journal, January 2014

Minimal cut sets in a metabolic network are elementary modes in a dual network journal, December 2011

Applications of genome‐scale metabolic reconstructions journal, January 2009

Optlang: An algebraic modeling language for mathematical optimization journal, January 2017

Minimal cut sets in biochemical reaction networks journal, January 2004

COBRApy: COnstraints-Based Reconstruction and Analysis for Python journal, January 2013

On Elementary flux Modes in Biochemical Reaction Systems at Steady State journal, June 1994

Computing the shortest elementary flux modes in genome-scale metabolic networks
journal, September 2009

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
journal, January 2014

Minimal cut sets in a metabolic network are elementary modes in a dual network
journal, December 2011

Applications of genome‐scale metabolic reconstructions
journal, January 2009

Optlang: An algebraic modeling language for mathematical optimization
journal, January 2017

Minimal cut sets in biochemical reaction networks
journal, January 2004

COBRApy: COnstraints-Based Reconstruction and Analysis for Python
journal, January 2013

On Elementary flux Modes in Biochemical Reaction Systems at Steady State
journal, June 1994