JSim, an open-source modeling system for data analysis

• DOI: 10.12688/f1000research.2-288.v3
• Publication Date: 2014-07-01T22:37:54Z
• Authors: Erik Butterworth; Bartholomew E. Ja...; Gary M. Raymond; Maxwell L. Neal; James B. Bassingt...
• Keywords: SBML

<ns4:p>JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological pharmacological systems through the testing of model solutions against data. It designed interactive, iterative manipulation code, handling multiple data sets parameter sets, making comparisons among different models running simultaneously or separately. Interactive use supported by large collection graphical user interfaces writing compilation diagnostics, defining input functions, runs, selection algorithms solving ordinary partial differential equations, run-time multidimensional graphics, optimization (8 methods), sensitivity analysis, Monte Carlo confidence ranges. JSim uses Mathematical Modeling Language (MML) declarative syntax specifying algebraic equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed procedure calls. MML simple, basically parameters variables, then equations straightforward, easily read understood mathematical form. This makes good teaching modeling as well analysis research. For high throughput applications, can be run batch job. automatically translate from repositories Systems Biology Markup (SBML) CellML models. Stochastic supported. supports assigning physical units to constants variables automates checking dimensional balance first step verification testing. Automatic unit scaling follows, e.g. seconds minutes, if needed. The Project File standard reproducible analysis: it includes one file everything analyzing set experiments: data, fitting, evaluation open source; about 400 human readable source physiological/biophysical available at<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://www.physiome.org/jsim/">http://www.physiome.org/jsim/</ns4:ext-link>.</ns4:p>