Tool stats & trends
Looking to identify usage trends or leading experts?
|Interface||Graphical user interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
|License||GNU General Public License version 3.0|
No version available
- person_outline Ines Thiele
Publication for rBioNet
Integration of a constraint based metabolic model of Brassica napus developing seeds with 13C metabolic flux analysis
[…] 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, […]
Computational Approaches for Microalgal Biofuel Optimization: A Review
[…] 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 […]
Proteomics based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca
[…] 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 […]
Modeling the Differences in Biochemical Capabilities of Pseudomonas Species by Flux Balance Analysis: How Good Are Genome Scale Metabolic Networks at Predicting the Differences?
[…] 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 […]
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 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 […]
Looking to check out a full list of citations?
Be the first to review rBioNet