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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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Documentation


Maintainer


  • person_outline Ines Thiele <>

Publication for rBioNet

rBioNet in publications

 (8)
PMCID: 4693189
PMID: 26516924
DOI: 10.3390/metabo5040659

[…] the focus on the biomass composition at the transition from day to night., modeling was performed using the cobra toolbox 2.0 [] with matlab 2013a 64 bit (the mathworks, inc., natick, ma, usa) and rbionet [] optimization using the cobra toolbox 2.0 and gurobi 5.6.0 []. a custom matlab script (see ) was used to generate the extended stoichiometric matrix from a cobra toolbox model structure., […]

PMCID: 4569355
PMID: 26367006
DOI: 10.1371/journal.pone.0137976

[…] were distributed into 5 different model compartments—glycosome, cytosol, mitochondrion, mitochondrial inter-membrane space and extracellular. all the above information was organized in the rbionet toolbox [] to eventually get an extensive model reconstruction ias142 for l. infantum energy metabolism. the model is available in the sbml format, ias142_recon.xml, for further reference […]

PMCID: 4271587
PMID: 25566296
DOI: 10.3389/fpls.2014.00724

[…] 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, […]

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 […]

PMCID: 3949408
PMID: 24653705
DOI: 10.3389/fphys.2014.00091

[…] module contains the improved reactions for the atb0,+ and bgt-1 transporters., the transport module was assembled according to the established reconstruction protocol (thiele and palsson, ) using rbionet as a reconstruction tool (thorleifsson and thiele, ). the functionality of reactions in the module, in conjunction with recon 2, was subsequently tested. all of the discussed modifications […]


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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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