SimBiology specifications


Unique identifier OMICS_11590
Name SimBiology
Software type Package/Module
Interface Command line interface, Graphical user interface
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes


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SimBiology in publications

PMCID: 5830403
PMID: 29491397
DOI: 10.1038/s41467-018-03139-6

[…] ated python script provided as ‘’. dependencies: tifffile, numpy, scipy, pandas, pillow, and scikits-image., model set-up: an ode-based compartmental model was constructed using the simbiology toolbox in matlab r2016a. three independent compartments corresponding to blood circulation, attachment/adherence substrate for cells and tissue parenchyma were defined in the model (fig. ) […]

PMCID: 5806446
PMID: 29497486
DOI: 10.4103/2045-9912.222449

[…] of the exhaled concentration to total body clearance., this study employs a physiologically based pharmacokinetic model developed by lockwood for anesthetic gases that has been employed within the simbiology toolbox of matlab (mathworks, natick, ma, usa). the model considers all transport to be perfusion limited, that there is no metabolism, and all excretion is through expiration via […]

PMCID: 5846846
PMID: 29146308
DOI: 10.1016/j.mad.2017.11.010

[…] relative and absolute tolerance set to 1e-06 and 1e-12 respectively and maximum internal steps set to 10000. parameter scans were performed in copasi. all stochastic simulations were run in matlab’s simbiology toolbox using the ssa solver. note that in all types of simulations, an acute stimulus was simulated as an event at a time point following the previous equilibration of the system […]

PMCID: 5739350
PMID: 29267273
DOI: 10.1371/journal.pcbi.1005874

[…] many other plsr models, using various combinations of the four model inputs. the fitness metrics for each model evaluated are given in ., all model equations were implemented in matlab using the simbiology toolbox. the final model is provided as the simbiology project file, as sbml, and as a matlab m-file (). parameter fitting was performed using the lsqnonlin function matlab. graphpad prism […]

PMCID: 5735807
PMID: 29258506
DOI: 10.1186/s12964-017-0207-9

[…] was formulated to describe the rate of change of the species’ concentration. the model is comprised of 53 odes to predict the concentrations of the 53 species in the signaling network over time. the simbiology toolbox (matlab) was used to implement the biochemical reaction equations, and the matlab stiff solver ode15s was used the numerically solve the system of odes. the model file is provided […]

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SimBiology institution(s)
The MathWorks, Meudon, France

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