I-1 Setting up the Operational Environment
Here are the preparations for using simBio. In simBio, Java is used for describing formulas, and XML is used for describing model structures. You need to set up the Java runtime environment to use simBio to run a simulation of a myocardial cell model, and to develop a myocardial cell model you need the Java development environment.
Provide a PC which can run Java 1.4.2 or greater. The PC which simBio was developed with is Windows XP, Pentium 4 2.4 GHz, RAM 512 MB. You can check the simBio operating environment below.
First, check that Java can be used. In the case of Windows, click on the [Start] button ->[All Programs]->[Accessories]->[Command Prompt]. Type java –version in the open window and press the Enter key, and if "java version 1.4.2" is displayed, then it is possible to use Java ( java is a command to run the Java program, –version is an option for displaying the version of Java which can be used. They are divided by a space.). When "java is not recognized as an internal or external command" etc. is displayed, please install Java from Free Java Download. When you click on "Download Now", latest version of J2SE Runtime Environment will be installed, but to create programs, JDK (Java Development Kit) is needed, so please select "JDK 6", and install.
Click on "Downloads" in http://eclipse.org/ and download the latest stable relase of eclipse SDK, and extract it into a suitable location. Here it is expanded in c:\. In the case of Windows XP, when you right click on the zip file, select "Extract All" and select c:\ as the folder extraction destination, the folder "c:\eclipse" will be created.
To edit XML files which are used in simBio, it is convenient if you have a suitable editor. Please download a file which matches the Eclipse version (for "eclipse SDK 3.2.2" this is currently "xmlbuddy_2.0.72.zip") from "XMLBuddy", and extract it to the Eclipse plugins folder (c:\eclipse\plugins). In the case of Windows XP, right click on the zip file, and select "Extract All". If you select the Eclipse plugin folder as the file extraction destination, the folder com.objfac.xmleditor_ 2.0.72 is created, and an environment for editing XML files is ready.
Eclipse Initial Settings
When you start eclipse.exe (c:\eclipse\eclipse.exe) which is in the eclipse folder, the Workspace Launcher Dialog asks which folder to use to save the programs which you will creates.
When you leave the default value as it is and press [OK], Eclipse starts, and a screen called "Welcome to Eclipse" appears. First, select [Window]->[Preferences...] to adjust the initial settings.
Set the character encoding to UTF-8
The simBio character code is UTF-8, so in [General]->Workspace dialog set [text/file/encoding] to UTF-8.
Separation of Source and Output Folders
In the [Java]->Build Path dialog, select [Folders] in [Source and output folder]. In [Source folder name] enter src/main/java, and in [Output folder name] enter target/classes.
Add tools.jar User Library
With Eclipse 3.3, in the Preferences dialog select [Java] -> [Build Path] -> [User Libraries]. Click [New...] and enter TOOLS as [User library name], and click [OK] to confirm. Click [Add JARs...] and in the file dialog open the file tools.jar found in the lib folder of installed jdk. Click [OK] to confirm.
XML Display Colour
In the initial settings of XMLBuddy, tags and attribute names are shown with the same colour. Let's try changing the colour to make it easier to see. Please select [XMLBuddy]→[XML]→[Colors]→[Attribute name], and choose a colour that you like.