To call C++ code from MML, see Calling C Code from MML. You should use only the C-compatible subset of C++ in the JSim API calls, although you may use the full power of C++ in any internal subroutines.

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Introduction

This document describes the process of calling Matlab computations within MML models. This is one of several ways to connect JSim and Matlab. For an overview of possible JSim/Matlab connection strategies, see Connecting JSim and Matlab.

Matlab is a matrix-based computational system distributed by The MathWorks(Natick, MA) and widely used for scientific computation. This document discusses several ways to use JSim and Matlab in conjunction to solve scientific problems. Both JSim and Matlab offer possibilities for graphic data display, however this document will focus on combining the computational power of the two products.

Currently there is no direct path from JSim MML to Fortran. Until such a time as there is, model writers should call C functions from MML and call Fortran functions from C using pre-compiled native libraries.

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Introduction

Antimony is a simple text language for specifying SBML style models. This document describes how to write Antimony models within JSim, and how to import and export Antimony files to and from JSim. This is not a tutorial of the Antimony language. For that, see the Antimony Home Page.

Antimony support within JSim is available for JSim version 2.03 and above.

Prerequisites:

Introduction

MML events model discrete changes of physical and physiological state such as voltage transitions, heart beats, etc. Events also provide a mechanism for calculation of recursive functions, such as Fibonacci numbers. Event-driven variables can freely intermix with continuous (e.g. ODE-calculated) variables, allowing you to model hybrid discrete/continuous systems.

Prerequisites:

This document is an introduction to building and running XSim-style models under JSim. This functionality is currently available only for JSim on Linux (i386) and MacIntosh.

Prerequisites:

Introduction

This document describes how to create the free-standing computational model code for an XSim-style model under JSim. It assumes you understand the Introduction to XSim-style models under JSim and are familiar with building Fortran programs on your system.

Contents

Writing & compiling Fortran model code

Wrapping your model code with jsxwrap

A simple example

Some caveats

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Introduction

This document describes the XSim template library for JSim, which is used to create the MML wrapper for an XSim-style model under JSim. It assumes you understand the Introduction to XSim-style models under JSim and are familiar with writing simple MML models under JSim.

Basics

More variable types

Spatial variables

Using units