Abstract
JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research. For high throughput applications, JSim can be run as a batch job. JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.
Highlights
The modeling of biological processes starts with defining the hypothesis to be tested in an experiment
In this article we describe the features of a simulation analysis system, JSim; it is the product of evolutionary improvements in the hypothesis testing cycle
JSim development efforts began in 1999 and augmented the functionality developed in SimCon and XSim by adding simplified model specification, facilities for data analysis and for distribution of results and of models, popular desktop and laptop support (Windows, Macintosh & Linux) and fully integrated multiprocessing for shared memory systems (Raymond et al, 2003)
Summary
Any reports and responses or comments on the article can be found at the end of the article. Partial differential and ordinary differential equations, differential algebraic equations (DAE), JSim, modeling, optimization, residuals, Monte Carlo, continuous systems, stochastic systems simulation, sensitivity, time series, reproducible research, SBML, CellML. We have added several new sections in response to reviewer’s comments: “Some Alternative Simulation Platforms”, “SED-ML Support” (in section “Future Plans”), “Code Verification” and “Using archived models for analyzing one’s own data”. Two new tables were added to the “Run-Time Performance” section. We have added clarifying wording in various places and 9 new references were included
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