meneco

meneco is a software tool for identifying and filling missing reactions to incomplete metabolic pathways. The meneco algorithm avoids stoichiometric constraints by formulating the problem as a qualitative combinatorial optimization problem.

Topic

Molecular interactions, pathways and networks;Endocrinology and metabolism

Detail

  • Operation: Metabolic network modelling;Metabolic labeling;Natural product identification

  • Software interface: Command-line user interface

  • Language: Python

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: French Government via the National Research Agency investment expenditure program IDEALG, the French national program EC2CO-MicrobiEn, CoMMERCE.

  • Input: -

  • Output: -

  • Contact: Anne Siegel anne.siegel@irisa.fr, Sylvain Prigent prigent@chalmers.se

  • Collection: -

  • Maturity: -

Publications

  • The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond
  • Prigent S, Collet G, Dittami SM, Delage L, Ethis de Corny F, Dameron O, Eveillard D, Thiele S, Cambefort J, Boyen C, Siegel A, Tonon T. The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. Plant J. 2014 Oct;80(2):367-81. doi: 10.1111/tpj.12627. Epub 2014 Aug 27. PMID: 25065645.
  • https://doi.org/10.1111/tpj.12627
  • PMID: 25065645
  • PMC: -
  • Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
  • Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T, Siegel A. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput Biol. 2017 Jan 27;13(1):e1005276. doi: 10.1371/journal.pcbi.1005276. PMID: 28129330; PMCID: PMC5302834.
  • https://doi.org/10.1371/journal.pcbi.1005276
  • PMID: 28129330
  • PMC: PMC5302834

Download and documentation

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