Download

CellDesigner 4.1beta

download from here in systems-biology.org.

Features

CellDesigner 4.1 beta is SBML Level 2 Version 4 Support + SABIO-RK Integration.
there are several new features and changes in CellDesigner 4.1 beta.
* Please note that this is the beta version, newly implemented features may not be fully functional.
* If you create/edit a file with this beta version, your model will not be able to open with the lower version of CellDesigner.

• Features 4.1beta

System Requirements

The current version of CellDesigner requires Java2 Runtime Environment (JRE1.5.0 or later) on

• Windows (XP or later)*
• MacOSX (10.4 or later)**
• Linux with X Window System ( Fedora Core 4 or later) ***

**On Windows Vista and 7, the installer is for 32 bit version.
**On Mac OS X 10.4 or later, Java 1.5.0_03 or later is required
*** On Linux platform, due to the version of native libraries, Fedora Core 4 or later is recommended; some problems will arise if you use other than these.

The installer includes JRE (Java Runtime Environment Version 6), so you do not have to install Java before your installation.

If SBW and its modules have already been installed, these modules are available. Especially time evolving simulation of the model being edited can be performed.

If you want to use Copasi (http://www.copasi.org) as an alternative solver, refer to Startup Guide (Sections 7.1 & 7.5) for setup.

Install

1. Install SBW and SBW modules

If you are interested in time evolving simulation and analysis on biochemical networks, we recommend you to install the Systems Biology Workbench (SBW) and SBW-powered software before you install CellDesigner.

To install SBW and SBW-powered software, follow their installation instructions.

If you would like to use CellDesigner alone right now, you can postpone this step until you need simulation and/or analysis.

• (*) As of Mar 2009, SBW 2.7.9 are available. For details on SBW information: http://sys-bio.org/research/sbwIntro.htm

2. Install CellDesigner

Download the one for your operating system and follow instructions provided in 00READEME.txt or Startup Guide to install CellDesigner for each environment.

The current release is distributed in archived installer package for each operating system.

• Windows: CellDesigner-41beta-windows-installer.exe
• MacOSX: CellDesigner-4.1beta-osx-installer.zip
• Linux:      CellDesigner-4.1beta-linux-installer.bin

* While J2RE is required for CellDesigner to run, the installers include it. Therefore, you do not need to download or install J2RE.

NOTICE: (2010/05/10) For Mac Snow Leopard (Mac OSX 10.6) Users
CellDesigner support 32 bit only. To run CellDesigner on Snow Leopard, you need to add -d32 option at Java VM startup.
from the command line from the CellDesigner directory:
"java -Djava.library.path=. -Xms32M -Xmx512M -d32 -cp $(ls exec/*.jar lib/*.jar | tr '\n' ':')
jp.sbi.celldesigner.Application"

NOTICE: (2010/03/04) For 64bit Windows Users
CellDesigner support 32 bit only. Please install CellDesigner onto 32 bit mode.

NOTICE: (2009/07/10) For Mac Leopard (10.5.7) Users
Due to the recent Mac Java update, there is a problem of CellDesigner launch. We will release the fixed version shortly. In the meantime, please download the following zip file, and execute the fix patch according to the 00Readme.txt in the zip file.
>>> cd401-leopard_java-fix.zip

NOTICE: (2009/01/26) For Ubuntu Linux Users
If compiz is enabled, it might cause the GUI problem. Please try the following commands to run CellDesigner:

$ export AWT_TOOLKIT="MToolkit"
$ ~/runCellDesigner4.0.

Documentation

• CellDesigner 4.1beta Startup Guide / [PDF Version]
• CellDesigner 4.0 : Running CellDesigner's Simulation using Control Panel / [PDF Version]
• CellDesigner 4.1beta : Plugin Tutorial / [PDF Version]
• CellDesigner Plungin API help (in your installed directory, /document/plugin/index.html)
• Help