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iBioSim specifications

Information


Unique identifier OMICS_04769
Name iBioSim
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0, MIT License
Computer skills Medium
Version 3.0.0
Stability Beta
Requirements
JRE, Graphviz
Maintained Yes

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Maintainer


  • person_outline Chris Myers <>

Publications for iBioSim

iBioSim in publications

 (7)
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] (kolpakov et al., ) is among the few tools that provide a full implementation of the sbml standard in terms of ode systems and also provides its functions as javascript api., the stand-alone tool ibiosim (myers et al., ) for modeling, analysis, and design of genetic circuits has been developed as an editor and simulator (ode and stochastic) with applications in systems biology as well […]

PMCID: 4246920
PMID: 25506588
DOI: 10.3389/fbioe.2014.00055

[…] to synthetic biology, a section of the journal frontiers in bioengineering and biotechnology., this paper describes a hierarchical stochastic simulation algorithm, which has been implemented within ibiosim, a tool used to model, analyze, and visualize genetic circuits. many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated […]

PMCID: 3846440
PMID: 24006914
DOI: 10.1186/1752-0509-7-88

[…] (ode) that represents the mathematical model. in order to compare simulation results of kinetic processes of the system, the mathematical models are solved using roadrunner [], copasi [], jsim [], ibiosim [], and jarnac [] simulation engines., for each test case, simulations of the computational models are obtained using the above-mentioned simulation environments with specific versions […]

PMCID: 3684516
PMID: 23663447
DOI: 10.1186/1754-1611-7-13

[…] genedesign (http://www.genedesign.org), genocad (http://www.genocad.org), genetdes (http://jaramillolab.issb.genopole.fr/display/sbsite/download), glamm (http://glamm.lbl.gov), ibiosim (http://www.async.ece.utah.edu/ibiosim), j5 dna assembly design automation software (http://j5.jbei.org/index.php/main_page), mathematica (http://www.wolfram.com/mathematica), mfold […]

PMCID: 3479904
PMID: 22683525
DOI: 10.1098/rsif.2012.0280

[…] computational tools and programming abstractions for synthetic biology are reviewed in purnick & weiss [], while languages for biological modelling more generally include antimony [], promot [], ibiosim [] and little b [], to name a few. more detailed comparisons between gec and other languages for synthetic biology are presented in pedersen & phillips [] and beal et al. []., […]


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iBioSim institution(s)
Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA; Department of Electrical and Computer Engineering, Utah State University, Logan, UT, USA; Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA; Raytheon BBN Technologies, Cambridge, MA, USA
iBioSim funding source(s)
Supported by the National Science Foundation under Grant No. CCF-1218095, CCF-1748200, and DBI-1356041.

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