This document describes some basics techniques for using ordinary differential equations (ODEs) within MML models.

Prerequisites:

• Introductory Survey of MML (required)
• Introduction to the JSim GUI (recommended)

Contents:

Introduction

This document describes using JSim MML's built-in integral() and sum() functions.

Prerequisites:

• Introductory Survey of MML (required)
• Introduction to the JSim GUI (recommended)

Contents:

Prerequisites:

• Introduction to the JSim GUI (recommended)
• Introduction to the JSim MML(recommended)

Contents:

Prerequisites:

• Introductory Survey of MML (required)
• Introduction to the JSim GUI (recommended)

Contents:

Introduction

This document is an introduction to Biological Component Librarys (BCLs), and their use in constructing JSim models.

Introduction

This document is a tutorial for writing JSim models using the MFAX Biological Component Library (BCL). MFAX stands for a Metabolite Flow and Exchange, and contains a set of components appropriate for chemical network models in multiple compartments with convective flow and membrane transport between those compartments.

Prerequisites:

• Using Templates in MML

Contents:

This document is the authoritative reference for the syntax and semantics of JSim's Mathematical Modeling Language (MML).

Prerequisites:

• Introductory Survey of MML (required)
• Introduction to the JSim GUI (recommended)

Contents:

This is a reference manual for the MFAX Biological Component Library (BCL). MFAX stands for a Metabolite Flow and Exchange, and contains a set of components appropriate for chemical network models in multiple compartments with convective flow and membrane transport between those compartments. This manual provides concise and exact syntax and semantics for each component.

Prerequisites:

The JSim Application Programmer Interface (API) is a set of documentation appropriate for creating Java code that interacts in useful ways with the JSim application.

Introduction

This document describes how to write JSim plugins, code modules that extend JSim's functionality at run-time. Familiarity with both JSim and Java software engineering is assumed.

Contents: