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Number of citations per year for the bioinformatics software tool SimBiology
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Protocols

SimBiology specifications

Information


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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No version available

SimBiology citations

 (20)
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‘Molecular habituation’ as a potential mechanism of gradual homeostatic loss with age

2018
Mech Ageing Dev
PMCID: 5846846
PMID: 29146308
DOI: 10.1016/j.mad.2017.11.010
call_split See protocol

[…] 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 to a stea […]

library_books

Trade off and flexibility in the dynamic regulation of the cullin RING ubiquitin ligase repertoire

2017
PLoS Comput Biol
PMCID: 5711038
PMID: 29149173
DOI: 10.1371/journal.pcbi.1005869

[…] The simulations depicted in were done using MatCont []. The transient simulations involving substrate degradation depicted in Figs and – were done using the SimBiology Toolbox of MATLAB []. Derivations of the analytical formulas in Eqs – can be found in . […]

library_books

Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi scale systems pharmacology approach

2017
PLoS Comput Biol
PMCID: 5560534
PMID: 28817561
DOI: 10.1371/journal.pcbi.1005650

[…] Plasma PK parameters are fit in SimBiology (MATLAB 9.1). We use a non-linear mixed effects model with a stochastic Expectation-Maximization (EM) algorithm assuming a constant error model and no covariates. The algorithm is run for 5 […]

library_books

The promises of quantitative systems pharmacology modelling for drug development

2016
Comput Struct Biotechnol J
PMCID: 5064996
PMID: 27761201
DOI: 10.1016/j.csbj.2016.09.002

[…] er . To describe a dynamic system, mathematical equations can be defined and solved in a wide variety of freely available environments such as Copasi , R  or Octave . Proprietary environments such as SimBiology® (part of MATLAB®) are also often used for model development. Finally, some commercial drug development programs specialise in predicting the ADME properties of compounds, like Simcyp  or G […]

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Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control

2016
Sci Rep
PMCID: 5017163
PMID: 27611502
DOI: 10.1038/srep33024
call_split See protocol

[…] The multi-level kinetic model for Synechocystis 6803 was developed and simulations were executed using the SimBiology toolbox of MATLAB (The MathWorks, Inc., Natick, Massachusetts, United States of America). The routine for parameter estimation was a hybrid genetic algorithm. The model for both high and am […]

library_books

A Model for the Application of Target Controlled Intravenous Infusion for a Prolonged Immersive DMT Psychedelic Experience

2016
Front Pharmacol
PMCID: 4944667
PMID: 27471468
DOI: 10.3389/fphar.2016.00211

[…] ed effects modeling (NON-MEM)—often give more reliable parameter estimates. These methods also allow identification of parameter covariates, such as weight or age (Mould and Upton, ).Using the Matlab Simbiology toolkit (Mathworks, Inc.), we fitted the 0.2 and 0.4 mg/kg time- series data separately. Both datasets were best fitted to a two-compartment model with enzymatic clearance, consistent with […]


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SimBiology institution(s)
The MathWorks, Meudon, France

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