Getting started with JSBML

The following are quick-start instructions for getting started with JSBML. Before doing any of the steps below, you will need to obtain a copy of JSBML either via the SourceForge download page or using SVN as described below.

Apart from this bref page, JSBML provides as well a nice User Guide with a chapter on getting started with JSBML. This chapter will be more up-to-date and detailled than the current page and will contain additional information to go behond the 'getting started' phase.

Introduction

JSBML is a library that will help you to manipulate SBML files. If you are not familiar with SBML, a good starting point would be to read the SBML specification. If you have some other questions about SBML, you may found the answer in the SBML FAQ.

JSBML is written in Java and to use it, you will need a Java Runtime Environment(JRE) 1.5 or higher. See for example the Java SE download page.

Using the JSBML JAR file distribution

Before starting to use JSBML, you will need to configure your CLASSPATH. JSBML provides you with two options :

• using the JSBML jar file with dependencies, then you just need to include this file in your CLASSPATH.
• using the JSBML jar file without dependencies, then you need to add all the needed dependecies of JSBML.

Using the JSBML JAR with dependencies

Using the JSBML JAR without dependencies

List of needed dependencies :

• biojava-1.7-ontology.jar : this is a stripped down version of the biojava-1.7 containing mostly ontology related classes.
• junit-4.8.jar
• stax2-api-3.0.3.jar
• staxmate-2.0.0.jar
• xstream-1.3.1.jar
• jigsaw-dateParser.jar : this is a stripped version of the jigsaw-TODO-version containing one class to manipulate date.
• log4j-1.2.8.jar
• stax-api-1.0.1.jar
• woodstox-core-lgpl-4.0.9.jar

These are the versions JSBML was developed and tested with, some more recent versions might work.

When you have all of these dependencies in your CLASSPATH alongside the jsbml jar file, you are ready to work with jsbml.

Using the source distribution

As an alternative to using the JAR files, you can check out the source tree from SVN and compile JSBML yourself. To do that, you will need to have a Java JDK installed, the Apache Ant build system, and Subversion, a version control system.

# to get the source
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk jsbml
cd jsbml

With the command above, you'll obtain the complete current source distribution of the JSBML project. If you are only interested in working with the SBML core, i.e., neither SBML extensions, nor JSBML modules, you may want

# to get the source of the JSBML core only
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/core jsbml-core
cd jsbml-core

# to compile and create the library jar file
ant jar

# to run the tests
ant test

Using JSBML extensions

To work with extension packages using JSBML, you can check out all packages at once

# Check out all JSBML extension packages as one repository:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/extensions JSBMLext

Or you can create a separate repository for each package you are interested in

# Download an individual extension package, for example the layout package:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/extensions/layout Layout

Here you can see all currently available SBML packages for JSBML.

Using JSBML modules

You can check out the modules of JSBML as follows:

# The module for using JSBML-based applications on Android OS can be obtained here:
 svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/android Android

# Obtain the CellDesigner bridge here:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/celldesigner celldesigner

# The JSBML/libSBML compare module contains test functions for comparion of both:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/compare compare

# And the libSBML compatibility module is available from this resource:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/libSBMLcompat libSBMLcomp

# The libSBML communication layer can be found here:
svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/libSBMLio/ libSBMLio