Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio

I-2 Getting simBio

Next, get simBio from the internet and set it in Eclipse as a Java project.

Getting source code via CVS

simBio's development is making progress on the "SourceForge" internet site, so connect to the SourceForge CVS from Eclipse, and get the source code.

SourceForge is a free service which provides a web-based environment for open-source software developers to handle project management in a coordinated yet simple way.
CVS is a system which manages the change history of source code. It saves code changes, and makes it easy to check parts which have changed, and return to an earlier version.
If you have problems connecting to "SourceForge" CVS due to firewall settings, then please read the "SourceForge" procedure, and try an http proxy, or follow the setting method for using a source package. You can set proxy information at [Window]->[Preferences...]->[Team]->[CVS]->Proxy Settings Dialog. Figure 1-2-a CVS proxy setting
  1. Select [Window]->[Open Perspective]->[Other...] from the Eclipse menu.
    Figure 1-2-1 Open the perspective
  2. Select [CVS Repository Exploring] in the perspective selection dialog, and click on [OK].
    Figure 1-2-2 Perspective Selection
  3. Right click on the empty area in the CVS repository view, and click on [New]->[Repository Location...].
    Figure 1-2-3 Registering a new location
  4. Enter simbio.cvs.sourceforge.net in the [Host] field, /cvsroot/simbio in [Repository path], and anonymous in [User], select pserver as the connection type and click on [Finish].
    Figure 1-2-4 Connection to SourceForge.net CVS
  5. If you can connect successfully, the CVS repository view location appears, and when you open [HEAD] you can see all the main project folders for simBio.
    Figure 1-2-5 SourceForge.net CVS
    means the place where the change history is saved. Where the configured server address, folders, user names, and connection method are all gathered is called the location.
  6. Open [Versions]->[simBio], select [simBio v_*], were * is the latest released version and right click.
    HEAD and version
    HEAD is where new features are added and mistakes are corrected with the most recent source code, and is always renewed. A version number is added when features are stable and it is released as a package.
  7. When you click on [Check Out] from the popup menu, code downloading begins.
    Figure 1-2-6 simBio CVS repository

Settings for using source packages

If you cannot connect to CVS from Eclipse, then use the simBio source release package.

The simBio source release package includes

  • docs_ja
  • JavaSpaces
  • JavaSpacesClient
  • RemoteClient
  • simBio

Where docs_ja is a project for documents in Japanese, simBio is the project for simBio itself and the other listed project folders are used for distributed computation, see JavaSpaces for more information.

Here we only describe how to create a new Eclipse project from existing source of the simBio project, however the process for the other four projects are the same.

  1. Access SourceForge simBio project from the web browser and download the file simBio-*.src.zip.
  2. Extract the simBio project folder from the file to the Eclipse workspace folder. Below is an example of the simBio project that has been extracted.
    Figure 1-2-7 workspace folder
    Extracted folder
    When the simBio project, which Eclipse extracted is not recognised, please check the folder. With the initial settings, the Eclipse workspace folder is C:\Documents and Settings\username\workspace. Please extract it so that the path is C:\Documents and Settings\username\workspace\simBio\.project.
  3. Select [File]->[New]->[Project...] from the menu.
    Figure 1-2-8 New Project Creation Menu
  4. Select [Java Project] with the new project dialog, and click on [Next].
    Figure 1-2-9 New Java Project Dialog
  5. Enter simBio in the [Project name] box, the same as the name of the extracted folder, and when you select [Finish] a project will be registered.
    Figure 1-2-10 Create simBio project

Checking simBio with the Java perspective

When the uptake has finished, select [Window]->[Open Perspective]->[Other...], select [Java] in the dialog and click on [OK].

When the "Welcome to Eclipse 3.2" screen appears, click on the arrow in the top right facing the back, and jump to [Workbench].

The simBio project is displayed in the Package Explorer view. Here simBio has been set as a project in Eclipse.

Figure 1-2-11 simBio project
Arrangment of Eclipse screens
You can refer to the guide from the [Help] menu for information about how to use Eclipse. You can arrange views in various places using drag and drop.
About Errors
If a red symbol is attached to a project in the Package Explorer view, then an error has occurred. Please check the error details by clicking on [Window]->[Show View]->[Problems].
When multiple errors occur, please check if the necessary libraries are recognized. Select the simBio project, open the menu with a right mouse click, and select the [Properties]->[Java Build Path]->[Libraries] tab. After deleting each displayed library (jar file group), select [Add JARS...], and select each library which is included in the lib folder. The libraries of JUnit3 and TOOLS should also be properly set. JUnit3 is a default library, but TOOLS should be added manually, see I-1 Add tools.jar User Library. The yellow ! symbol is a warning. Please display the Problems view and check the details. Note that there can be many warning messages for the project without hindering operations.
Figure 1-2-12 Setting libraries (jar files) in the build path

JDK Compliance Settings

The Eclipse JDK Compliance Settings need to be changed from it's default settings and set as the figure below show, if JDK 1.4 is used. In Eclipse choose the menu [Window] in Eclipse and [Preferences...] and in the preference menu choose [Java] -> [Compiler]. The settings may have a different place depending on Eclipse version. This is how JDK Compliance Settings are found in Eclipse Europa (3.3).

Figure 1-2-13. JDK Compliance Settings (the screen capture are made in Eclipse Europa (3.3), package Eclipse IDE for Java EE Developers)