iBioSim statistics

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Citations per year

Number of citations per year for the bioinformatics software tool iBioSim
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Tool usage distribution map

This map represents all the scientific publications referring to iBioSim per scientific context
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Associated diseases

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Popular tool citations

chevron_left Quantitative kinetic modeling Circuit design chevron_right
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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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Versioning


No version available

Documentation


Maintainer


  • person_outline Chris Myers

Publications for iBioSim

iBioSim citations

 (9)
library_books

Toward community standards and software for whole cell modeling

2016
IEEE Trans Biomed Eng
PMCID: 5451320
PMID: 27305665
DOI: 10.1109/TBME.2016.2560762

[…] re tools such as CellDesigner [] and VANTED [], and (3) writing scripts to generate SBML from the diagrams. Other groups used model design tools such as Antimony [], BioUML [], COBRApy [], COPASI [], iBioSim [], and libRoadRunner [] to recode submodels based on the original documentation. A few of the groups encoded submodels by converting the MATLAB code to SBML. As an example, and File S1 illus […]

library_books

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3

2015
J Integr Bioinform
PMCID: 5451323
PMID: 26528566
DOI: 10.2390/biecoll-jib-2015-268

[…] a revised draft specification issued in 2012. Smith then worked on implementating this draft specification in libSBML and integrating it into Antimony, and Chris Myers worked on integrating it into iBioSim. As a result of these experiences, additional issues became apparent and were discussed during HARMONY 2012. Those dicussions produced the following conclusions and changes:The use of ports is […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

2014
Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] ioUML (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 as synth […]

library_books

Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

2014
Front Bioeng Biotechnol
PMCID: 4246920
PMID: 25506588
DOI: 10.3389/fbioe.2014.00055

[…] cess in the electrical engineering field in the construction of complex circuits, the synthetic biology field has introduced the development of genetic design automation (GDA) tools (Myers et al., ). iBioSim, being developed at the University of Utah, is one example of such a tool (Madsen et al., ). The iBioSim tool can be used to model, analyze, and visualize genetic circuits. Models in iBioSim a […]

library_books

Parts and Pools: A Framework for Modular Design of Synthetic Gene Circuits

2014
Front Bioeng Biotechnol
PMCID: 4186347
PMID: 25340051
DOI: 10.3389/fbioe.2014.00042

[…] s of gene digital circuit design should be enabled to produce not only abstract schemes but also actual gene gates. This might be achieved through a Directed Acyclic Graph (DAG)-based approach [as in iBioSim (Roehner and Myers, )] by using the signal separation in Eq. () as a cost function to be optimized. […]

library_books

An online model composition tool for system biology models

2013
BMC Syst Biol
PMCID: 3846440
PMID: 24006914
DOI: 10.1186/1752-0509-7-88

[…] ns (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 as shown […]


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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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