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SBMLToolbox specifications

Information


Unique identifier OMICS_06013
Name SBMLToolbox
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline SBMLToolbox Team <>

Publication for SBMLToolbox

SBMLToolbox in publications

 (5)
PMCID: 5929573
PMID: 29672509
DOI: 10.1371/journal.pgen.1007357

[…] were performed in matlab 2017a (mathworks) with scripts from the cobra toolbox (downloaded may 12, 2017 from the opencobra repository) [], and using the gurobi 7.0.2 solver (gurobi.com), the sbmltoolbox 4.1.0 [], and libsbml 5.13.0 []. boundary conditions for simulation of the defined medium are given in . single and double gene deletion analyses were performed using […]

PMCID: 5864417
PMID: 29577088
DOI: 10.1128/mSystems.00170-17

[…] et al. and found to be 1,060 mmol atp gdcw−1 h−1 (). the genome-scale models were formatted in systems biology markup language (sbml) level 3 version 1.0 (sbml.org) and was read into matlab using sbmltoolbox (version 4.1) () and libsbml (version 5.6.0) (). the model files in excel format are available in the supplemental material, and sbml, gams, and matlab files are available at github […]

PMCID: 4219680
PMID: 25368989
DOI: 10.1371/journal.pone.0110380

[…] struggle with compatibility to a biological context due to the scale and stochastic nature of systems biology., although there exists efforts at model refinement protocols with tools such as sbmltoolbox and cobra toolbox, performing these manual refinement methods can take months to a year –. our work on a diagnostic application offers algorithms to narrow the scope of areas requiring […]

PMCID: 3410817
PMID: 22687330
DOI: 10.1186/1687-4153-2012-6

[…] coli using standard molecular biology methods []. its development is a milestone in synthetic biology. we have obtained the model as an sbml file in xml format [-]. we have used the libsbml [] and sbmltoolbox [] libraries to interpret the model and incorporate it to our own manipulation and simulation toolbox for phase computations. the period of the continuous oscillator obtained […]

PMCID: 2850882
PMID: 20230629
DOI: 10.1186/1752-0509-4-23

[…] code was translated into the jacobian language (numerica technology, cambridge, ma) using a translator written in matlab (the mathworks, natick, ma) using the sbml toolbox http://sbml.org/software/sbmltoolbox/. scripts were written in jacobian and matlab to generate dose-response curves and figures. model files are available in additional files , , and . ic50's were calculated using graphpad […]


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SBMLToolbox institution(s)
Science and Technology Research Institute, University of Hertfordshire Hatfield, UK

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