=====================================
CellDesigner(TM)  installer package

The Systems Biology Institute
Keio University
Mitsui Knowledge Industry
Mizuho Information & Research Institute

February 1st, 2013

[version_number] = 4.3
libSedML + libSBGN-ML + SABIO-RK reaction information import function update + bug fixes
=====================================

Thank you for trying CellDesigner.
This document contains the instruction on CellDesigner installation/setup and some useful information on the software.

========
Contents
========
I.	Operating Environment
II.	Install SBW and SBW Modules
III.	Install CellDesigner
IV. 	Startup CellDesigner
V. 	Useful Information
VI.	Release Information / Bug Fixes
VII.    File Compatibilities


==================================
I.	Operating Environment
------------------------------------------------------------
- Windows (XP or later) 32bit only 
- MacOSX (10.6 or later) 32bit, 64bit*
- Linux with X Window System (Fedora Core 4 or later) 32bit, 64bit

*On Windows Vista and above, the installer is for 32 bit version.
For 64bit Windows Users, CellDesigner supports 32bit only. Please install CellDesigner onto 32bit mode.

*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.

*On Mac OS X 10.6 or later, Java 1.6.0 or later is required. 

The installer includes JRE (Java Runtime Environment 1.6), 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 on Windows, please download "Visual Studio 2010 runtime (Visual C++ 2010 runtime)" to use Copasi from CellDesigner.

====================================
II.	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 (*).
Please check http://sys-bio.org/ and download the software from Software Downloads section.

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 February 2012, SBW 2.9.0 is available for Windows, MacOSX and Linux.
    For details on SBW information: http://sbw.sourceforge.net/

(**) Note: In case you have installed SBW 2.7.6 or later, and you encounter an error while installing CellDesigner, there might be a possibility that the C++ Broker is up which prevents CellDesigner to start. Please try to kill the broker using the Task Manager, or restart your system before you resume the CellDesigner installation.


==================================
III. Install CellDesigner
------------------------------------------------------------
The current release is distributed in archived installer package for each operating system.

Windows: CellDesigner-43-windows-installer.exe
MacOSX:  CellDesigner-4.3-osx-installer.dmg
Linux:   CellDesigner-4.3-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. 

Windows: --------------------------
1.	Double click CellDesigner-43-windows-installer.exe.
The installer window should open, and follow the message therein.

Note: For 64bit Windows users, please install CellDesigner onto 32 bit mode.

MacOSX: ------------------------------
1.	Double click CellDesigner-4.3-osx-installer.dmg. 
2.	The .dmg file should automatically be mounted and a Finder window should open in which CellDesigner-4.3-osx-installer exists. 
Then double click it.
The installer window should open, and follow the message therein.

Linux: ------------------------------------
1.	Open a shell and, cd to the directory where you downloaded the installer. 
2.	At the prompt type: 
    % chmod u+x CellDesigner-4.3-linux-installer.bin
    % ./CellDesigner-4.3-linux-installer.bin
The installer window should open, and follow the message therein.    

Note: For 64bit Linux Users, please install CellDesigner onto 32 bit mode. 
* How to install CellDesigner4.2 on 64bit Linux
 1. Install "LSB (Linux Standard Bas)" if not installed on your system
 2. Install "ia32-libs" if not installed on your system
 3. Launch CellDesigner4.2-Installer with following command:
     $ ./CellDesigner-4.2-linux-installer.bin --mode xwindow

 [Installed File Images]
--------------------------------
After installation finished, you would see the following directories/files in the installation directory (CellDesigner4.1.1 by default).

+00README.txt
|
+CellDesigner4.3.exe	executable application module (* Windows only)
+CellDesigner4.3.sh	executable application module (* Linux only)
+CellDesigner4.3	executable application module (* Mac OS X only)
|
+/documents
| +ControlPanel42.pdf	quick tutorial for control panel
| +PluginTutorial42.pdf	quick tutorial for plug in
| +StartupGuide43.pdf	this document
| +/plugin
|   +index.html	Plug-in API document
|
+/exec
| +autolayout_yobf.jar
| +celldesigner.jar 	library for CellDesigner application
| +yObf.jar
|
+/jre (1.6) 	*(Windows, Linux only)
|
+/lib
| +ant-schematron.jar
| +avalon-framework-4.1.4.jar
| +axis.jar
| +batik.jar
| +browserlauncher.jar
| +collections-generic-4.01.jar
| +commons-discovery-0.2.jar
| +commons-logging-1.0.4.jar
| +commons-math-2.2.jar
| +concurrent.jar
| +copasi.jar
| +copasi_gui.jar
| +customiser.jar
| +freehep-export-2.0.3.jar
| +freehep-graphics2d-2.0.jar
| +freehep-graphicsio-2.0.jar
| +freehep-graphicsio-ps-2.0.jar
| +freehep-io-2.0.1.jar
| +freehep-swing-2.0.2.jar
| +freehep-util-2.0.1.jar
| +icu4j_3_4.jar
| +iri.jar
| +itext-1.4.6.jar
| +jai_codec.jar
| +jai_core.jar
| +jakarta-oro.jar
| +jaxen-1.1.1.jar
| +jaxrpc.jar
| +jcommon-1.0.0-pre2.jar
| +jdom-contrib.jar
| +jdom.jar
| +jena.jar
| +jersey-client-1.2.jar 
| +jersey-core-1.2.jar
| +jeuclid-2.0.jar
| +jfreechart-1.0.0-pre2.jar
| +jlibsedml.jar
| +jmathml.jar
| +jmf.jar
| +jsbml-1.0-a1-with-dependencies.jar
| +jsr311-api-1.0.jar
| +junit-4.1.jar
| +log4j-1.2.12.jar
| +mediaplayer.jar
| +miglayout-4.0-swing.jar
| +mlibwrapper_jai.jar
| +MRJAdapter.jar
| +multiplayer.jar
| +openide-lookup-1.9-patched-1.0.jar
| +org.sbgn.jar
| +pantherConverter.jar
| +poi-3.0-rc4-20070503.jar
| +quaqua-filechooser-only.jar
| +saaj.jar
| +sabiows.jar
| +saxon9he.jar
| +sbmlj.jar
| +SBWCore.jar
| +SimulationCoreLibrary_v1.1_slim.jar
| +SOSlib.jar
| +wsdl4j-1.5.1.jar
| +xercesImpl.jar
| +xml-apis.jar
| +xom-1.2.1.jar
|
+bzip2.dll			*(Windows only)
+CopasiJava.dll		*(Windows only)
+libexpat.dll		*(Windows only)
+libsbml.dll		*(Windows only)
+sbmlj.dll			*(Windows only)
+SOSlibJava.dll		*(Windows only)
+zlib1.dll			*(Windows only)
|
+libbz2.so.1		*(Linux only)
+libCopasiJava.so	*(Linux only)
+libexpat.so.1		*(Linux only)
+libexpat.1.dylib	*(Linux only)
+libsbml.so			*(Linux only)
+libsbmlj.so		*(Linux only)
+libSOSlib.so		*(Linux only)
+libz.so.1			*(Linux only)
|
+libbz2.1.0.dylib		*(Mac OS X only)
+libCopasiJava.jnilib	*(Mac OS X only)
+libexpat.1.dylib		*(Mac OS X only)
+libquaqua64.jnilib		*(Mac OS X only)
+libsbml.dylib			*(Mac OS X only)
+libsbmlj.jnilib		*(Mac OS X only)
+libSOSlibJava.jnilib	*(Mac OS X only)
+libz1.dylib			*(Mac OS X only)
|
+/licenses
| +/celldesigner
|   +license.txt
| +/libraries
|   +axis.LICENSE.txt
|   +batik.LICENSE.txt
|   +batik.NOTICE.txt
|   +FreeHEP.LGPL.txt 
|   +FreeHEP.LICENSE.txt
|   +itext-MPLICENSE.txt
|   +jai.LICENSE.txt
|   +jfreechart.LICENSE.txt
|   +libsbml.LICENSE.txt
|   +mrjadapter.LICENSE.txt
|   +quaqua.LICENSE.html
|   +xerces.LICENSE.txt
|   +xercesImpl.LICENSE.txt
|   +xercesImpl.NOTICE.txt
|   +xml-apis.LICENSE-SAX.html
|   +xml-apis.LICENSE.DOM-documentation.html
|   +xml-apis.LICENSE.DOM-software.html
|   +xml-apis.LICENSE.txt
|   +xml-apis.NOTICE.txt
|   +yfiles-3rdPartyLicenses.html
|   +yfiles-GeneralLicenseTerms.html
|   +yfiles-GeneralTermsandConditions.html
|
+/Microsoft.VC80.CRT		*(Windows only)
| +Microsoft.VC80.CRT.manifest
| +msvcm80.dll
| +msvcp80.dll
| +msvcr80.dll
|
+/plugin	compiled plugin jar files are added in this directory
| +MappingArrayMass_plugin.jar
|
+/samples
| +components42.xml 	sample for various components
| +database.xml	sample for database connections
| +M-Phase2.xml 	sample for model editing
| +Macros.xml 	sample for macros
| +MAPK42.xml 	sample for simulation provided by SBML ODE Solver
| +SBGN_RefCard.xml	CellDesigner4.2 notation against SBGN Process Diagram Level 1 reference card
| +sim1.xml		sample for simulation
| +sim2.xml		sample for simulation with annotation
| +unitOfInformation.xml		CellDesigner4.2 notation on unit of information
| +/nbt	sample files used in Nature Biotech paper by Kitano
| +/notation	sample files for notation
| +/plugin	sample source and jar files for plugin
| +/sbml	sample files from SBML L2V4 documents
|
+ mmlctop2_0.xsl
+ sbgn_pd.sch
+ SBGN.xsd
|
+uninstall.exe	*(Windows only)
+uninstall		*(Linux only)
+Uninstaller	*(Mac OS X only)


==================================
IV. Startup CellDesigner
------------------------------------------------------------
Windows: ----------------------------------
1.	Double click shortcut icon   CellDesigner4.3 in your desktop. 
Or double click CellDesigner4.3.exe in the directory where you chose to install (C:\Program Files\CellDesigner4.3 by default).

MacOSX: ------------------------------------
1.	Double click CellDesigner in the folder you chose to install (Application/CellDesigner4.3 in you home directory by default).

Linux: ----------------------------------------
1.	On a shell, cd to the directory where you chose to create links and type ./runCellDesigner4.3
Or type ./runCellDesigner4.3 after cd to the directory where you chose to install (CellDesigner4.3 in you home directory by default).


====================================
V. Useful Information on CellDesigner
----------------------------------------------------------------
To use CellDesigner, 

	see startupguide43.pdf in documents folder.

To use Control Panel from CellDesigner, 

	see controlpanel42.pdf in documents folder.

To use Plugin of CellDesigner, 

	see plugintutorial42.pdf in documents folder.
        http://celldesigner.org/plugins.html

Online Help

	http://celldesigner.org/help/

News and useful information including Tutorial materials

	http://celldesigner.org/

Any Inquiries on CellDesigner: 
	
	info@celldesigner.org

====================================
VI. Release Information / Bug Fixes
----------------------------------------------------------------
New feature and changes in CellDesigner 4.3 are as follows:

[New Features]
- SBGN-ML export support
- SABIO-RK new user interface
- Simulation Core Library in replacement of JSBML simulation library

[Updates in CellDesigner 4.3]
-libSedML library
-SBO export
-MIRIAM resource list
-Sample Files (to store updated SBO terms)

[Bug Fixes in CellDesigner 4.3]
- Fixed SedML file export

[Known problems]
- Copasi GUI: focus out from Copasi panel when the mouse pointer moves out
- SBW connection: Some SBW modules may not work correctly

====================================
VII. File Compatibilities
----------------------------------------------------------------
When you read the files created by lower version of CellDesigner, 
CellDesigner 4.3 validates the file using libSBML consistency check utility.

1, Open a file created by lower version of CellDesinger.
2. Compartment's size attributes are automatically updated.
3. File conversion needed dialog is open.
   "The file seems to be created by lower version of CellDesigner.
   Do you want to convert this model to work with the current version?"
4. The file is converted and open with CellDesigner4.3.

With CellDesigner 4.0:
Due to the CellDesigner 4.0 new notation scheme, 
the following components are no longer supported.
Please edit the original files and redraw them with 4.2 components.

-Transcriptional activation -> catalysis shape
-Transcriptional inhibition -> inhibition shape
-Translational activation   -> catalysis shape
-Translational inhibition   -> inhibition shape

- Tag (4.0 beta files only) -> cannot open file. 
  * delete it with 4.0beta and reopen it with CellDesigner4.0.


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Copyright 2005-2013 The Systems Biology Institute, Tokyo Japan.  All rights reserved.