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modelBorgifier specifications

Information


Unique identifier OMICS_20096
Name modelBorgifier
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Joerg Buescher

Additional information


https://opencobra.github.io/cobratoolbox/latest/modules/modelBorgifier.html

Publication for modelBorgifier

modelBorgifier citations

 (2)
library_books

Genome Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

2016
PLoS One
PMCID: 4859558
PMID: 27152931
DOI: 10.1371/journal.pone.0155038

[…] action associations and expanded each reaction into several reactions, each under the control of only one enzyme. We reconciled the reference network’s metabolite and reaction abbreviations using the modelBorgifier Toolbox []. We used iRC1080 as the template model and subsequently compared iJN678 and Knoop to the template model.Starting from the P. tricornutum genome annotation Phatr2 (Phatr3 was […]

library_books

Integration and Validation of the Genome Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism

2016
PLoS One
PMCID: 4734642
PMID: 26812499
DOI: 10.1371/journal.pone.0148031

[…] This step not only allowed unifying metabolite names but also to include its molecular formula and charge at pH 7.2.Once all metabolite names were unified, PpaMBEL1254 and iPP668 were compared using ModelBorgifier [], thereby obtaining a first pre-merged model. In a second step, this merged model was compared to iLC915, generating a first draft of the consensus model. Due to important differences […]


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modelBorgifier institution(s)
BRAIN Aktiengesellschaft, Microbial Production Technologies, Platform for Quantitative Biology and Sequencing, Zwingenberg, Germany
modelBorgifier funding source(s)
Supported by German Academic Exchange Service (DAAD) through a RISE professional scholarship.

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