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Meneco specifications

Information


Unique identifier OMICS_21467
Name Meneco
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.5.0
Stability Stable
Requirements
pip, PyASP
Source code URL https://codeload.github.com/bioasp/meneco/zip/meneco-1.5.2
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Anne Siegel
  • person_outline Sylvain Prigent

Publications for Meneco

Meneco citations

 (3)
library_books

Analysis of Piscirickettsia salmonis Metabolism Using Genome Scale Reconstruction, Modeling, and Testing

2017
Front Microbiol
PMCID: 5732189
PMID: 29321769
DOI: 10.3389/fmicb.2017.02462

[…] eaction associations from transport reactions were re-evaluated based on gene annotations and BLAST searches against the Transport Classification Database TCDB. Network gap-filling was done using the meneco tool () and the BiGG database as a source for additional reactions. This tool does topological gap-filling, searching for reactions whose incorporation in the draft model can complete paths fro […]

library_books

Reconstruction of the microalga Nannochloropsis salina genome scale metabolic model with applications to lipid production

2017
BMC Syst Biol
PMCID: 5496344
PMID: 28676050
DOI: 10.1186/s12918-017-0441-1

[…] ted compartments, changed reversibility for some reactions, moved species among compartments, renamed and pruned unused elements, among other changes. In order to generate a functional model, we used meneco [, ] to look for BiGG reactions that could fill gaps in the model. meneco provided us with candidate reactions that were handed to the manual curators, who approved their inclusion into the mod […]

library_books

Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

2014
Front Genet
PMCID: 4110880
PMID: 25120558
DOI: 10.3389/fgene.2014.00241

[…] nantes.fr/cgi-bin/portal.py#forms::memerge). In the context of this study, we refer to this merged network as the “holobiont network.” Following the procedure outlined on the EctoGEM website, we used Meneco 1.4.1 (https://pypi.python.org/pypi/meneco) to test the capacity of the holobiont network to produce 50 target metabolites that have previously been observed in xenic E. siliculosus cultures (G […]

Citations

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Meneco institution(s)
Institute for Research in IT and Random Systems - IRISA, Université de Rennes 1, Rennes, France; Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden; Irisa, CNRS, Rennes, France; Dyliss, Inria, Rennes, France; Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France; Computer Science Laboratory of Nantes Atlantique - LINA UMR6241, Université de Nantes, Nantes, France; Molecular Genetics, Genomics and Microbiology - GMGM, Université de Strasbourg, Strasbourg, France, CNRS, Strasbourg, France
Meneco funding source(s)
Supported by the French Government via the National Research Agency investment expenditure program IDEALG ANR-10-BTBR-04; and the French national program EC2COMicrobiEn, CoMMERCE.

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