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rBioNet specifications

Information


Unique identifier OMICS_14732
Name rBioNet
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Requirements
COBRA toolbox
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Ines Thiele

Publication for rBioNet

rBioNet citations

 (5)
library_books

Integration of a constraint based metabolic model of Brassica napus developing seeds with 13C metabolic flux analysis

2014
Front Plant Sci
PMCID: 4271587
PMID: 25566296
DOI: 10.3389/fpls.2014.00724

[…] 2 reactions and 2032 genes for Arabidopsis, leaving the arduous task of model refinement to the reconstructionist. Other platforms have been designed for model building and curation. For example, the rBioNet extension for COBRA offers a convenient graphical user interface for quality control and assurance (Thorleifsson and Thiele, ). While clearly there are many options for the reconstructionist, […]

library_books

Computational Approaches for Microalgal Biofuel Optimization: A Review

2014
Biomed Res Int
PMCID: 4189764
PMID: 25309916
DOI: 10.1155/2014/649453

[…] mple, BioCyc, MetaCyc [], KEGG (Kyoto Encyclopedia of Genes and Genomes) [], Reactome [], and BiGG [] can be named. In turn, common metabolic reconstruction tools include COBRA (more specifically its rBioNet component) [–], Model SEED [], and Pathway Tools [].Pathway Tools [, ] is an integrated software tool that can create in a semiautomated manner organism-specific network and pathways databases […]

library_books

Proteomics based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

2014
BMC Syst Biol
PMCID: 4236713
PMID: 25115351
DOI: 10.1186/s12918-014-0086-2

[…] to understand the underlying metabolic pathways and network in T. fusca[],[],[]. The reaction database used for drafting the model includes but is not limited to sources such as KEGG [],[], BiGG [], rBioNet [], UniProt [] and MBRole []. Information from disparate databases were tabulated to form an in-house reaction database as illustrated in Figure .The process of compiling biochemical reactions […]

library_books

Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome Scale Metabolic Networks at Predicting the Differences?

2014
Sci World J
PMCID: 3953581
PMID: 24707203
DOI: 10.1155/2014/416289

[…] iling the metabolism of an organism to a machine-readable format. There are various ways to reconstruct a model ranging from bottom up, totally manual approach [] to the semiautomated process such as rBioNet [], GEMSiRV [], and RAVEN []. Available genome-scale metabolic network models have a wide spectrum from bacteria [–], to archaea [], and to mammals and human [–].The common point of the all re […]

library_books

Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

2014
J Cheminform
PMCID: 3917611
PMID: 24468196
DOI: 10.1186/1758-2946-6-2

[…] of metabolites, with multiple identifiers each, is extremely laborious. Metabolites in early reconstructions were generally annotated manually. Today, reconstruction tools such as the Model SEED [], rBioNet [] and the SuBliMinaL Toolbox [] facilitate the process by populating new reconstructions with pre-annotated components from source databases. Metabolites in the source databases, however, may […]

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rBioNet institution(s)
Center for Systems Biology, University of Iceland, Reykjavik, Iceland; Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland
rBioNet funding source(s)
This work was supported by Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery through Advanced Computing program (grant DE-SC0002009); European Research Council (grant proposal no. 232816); Rannis Nyskopunarsjodur namsmanna.

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