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JSim specifications


Unique identifier OMICS_21416
Name JSim
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.17
Stability Stable
Source code URL http://www.physiome.org/jsim/download/source.html
Maintained No




No version available


Publication for JSim

JSim citations


A Multi Institutional Comparison of Dynamic Contrast Enhanced Magnetic Resonance Imaging Parameter Calculations

Sci Rep
PMCID: 5593829
PMID: 28894197
DOI: 10.1038/s41598-017-11554-w

[…] ns, resulting in 30 different Ktrans-ve pairs, each encompassing 10 × 10 pixels. The Ktrans and ve values were used to generate synthetic image data using the Tofts-Kermode two-parameter model run in JSim, an open-source modeling system,. One DRO without noise and 28 DROs with noise (SNR 0.18–1.8) simulated by varying the sampling interval, timing offset, S0, and sigma value were used to evaluate […]


Semantics Based Composition of Integrated Cardiomyocyte Models Motivated by Real World Use Cases

PLoS One
PMCID: 4696653
PMID: 26716837
DOI: 10.1371/journal.pone.0145621

[…] ation, SemGen, available at http://sbp.bhi.washington.edu/projects/semgen. SemGen provides utilities for annotating existing models encoded in CellML [], Systems Biology Markup Language (SBML) [] and JSim’s Mathematical Modeling Language (MML) [] as well as utilities for extracting out parts of models and merging models into new systems. Our goal with SemGen is to provide a tool that facilitates b […]


Implementation of a Model of Bodily Fluids Regulation

Acta Biotheor
PMCID: 4531145
PMID: 25935135
DOI: 10.1007/s10441-015-9250-3

[…] tabolic networks and models of cell signal transduction, the CellML repository contains several hundred marked-up legacy models (mostly at the level of membrane transport or signal transduction), the JSim Consolidated Model Database indexes 73390 models across five archives, and annotation tools such as the RICORDO resource (de Bono et al. ) and the ApiNATOMY (de Bono et al. ) project now facilita […]


OpenCOR: a modular and interoperable approach to computational biology

Front Physiol
PMCID: 4319394
PMID: 25705192
DOI: 10.3389/fphys.2015.00026

[…] wn CellML API) or their own CellML import mechanism tend to support only CellML 1.0. This is the case, for example, with CESE (cese.sourceforge.net), Chaste (Mirams et al., ; www.cs.ox.ac.uk/chaste), JSim (Butterworth et al., ; physiome.org/jsim), Myokit (Clerx et al., ; myokit.org) and VCell (Moraru et al., ; vcell.org). […]


Diverse Data Sets Can Yield Reliable Information through Mechanistic Modeling: Salicylic Acid Clearance

PMCID: 4905731
PMID: 27308260
DOI: 10.9734/BJPR/2015/19156

[…] We used a general-purpose simulation system, JSim [], designed for data analysis, displaying results and storing them as Reproducible Exchange Packages (REP). JSim code for the three models is written in MML, Mathematical Modeling Language: the […]


Improving Collaboration by Standardization Efforts in Systems Biology

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

[…] lternative is libRoadRunner, a highly performant C++ library for the simulation of SBML models, which provides automatically generated language-bindings to Python (Sauro et al., ).The Java-based tool JSim has been designed for building quantitative numeric models as well as the analysis of these models based on given experimental data (Butterworth et al., ). It supports ODEs and PDEs, discrete eve […]


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JSim institution(s)
Department of Bioengineering, University of Washington, Seattle, WA, USA
JSim funding source(s)
Supported by NIH grants HL9719, RR1243, EB1273, HL073598, EB8407, and GM094503 and NSF grant 0506477.

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