A portal site for systems biology.

Features:
CellDesigner 4.0 beta is the enhanced Graphical Notation version, based on SBGN Level 1 draft. There are several new features and changes in CellDesigner 4.0 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.

Operating Environment:

Windows (2000 or later) MacOSX (10.4 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner3.5.2 is the bug fix version of CellDesigner 3.5.1.





Operating Environment:

Windows (2000 or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later)

>>Install Instructions

Features:
CellDesigner3.5.1 is the bug fix version of CellDesigner 3.5.






Operating Environment:

Windows (2000 or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner 3.5 now supports smooth SBML file handling. Validate and auto-layout when opening a SBML file, simulate and output to PDF for your publication.




Operating Environment:

Windows (2000 or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner 4.0 alpha is the Plugin Developer's version. If you can use Eclipse, you can develop your own plugin onto CellDesigner. Other than Plugin function, there are several new features and changes in CellDesigner 4.0 alpha.
* Please note that this alpha version, newly implemented features may not be fully functional.


Operating Environment:

Windows (2000 or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner3.2 now support libSBML, a standard SBML library. You can handle files smoothly from modelling to simulation. It also supports Java 5 and Intel Mac.




Operating Environment:

Windows (2000 or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner3.1 is the speed up version of CellDesigner 3.0.1.
Ver.3.1 aims to achieve smoother, user friendly operation: performance tuning for displaying graphics on canvas, navigation using Bird's Eye View, and wheel mouse,and directly import curated models from BioModels.net database.


Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner3.0.1 is the bug fix version of CellDesigner 3.0.





Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
A new notation that enhanced previous process diagram into gene and RNA, as well as protein complex structure. Version 3.0 implements most part of notations described in Kitano, et al., "Using Process Diagram for Graphical Representation of Biochemical Networks", Nature Biotechnology, August 2005.


CellDesigner3.0 supports simulation and parameter scan by an
integration with SBML ODE Solver. By using CellDesigner3.0, you can browse and modify existing SBML models, create a new model with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.

Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:

Simulation and parameter scan feature by an integration    with SBML ODE Solver (Thanks to Rainer Machne and Christoph Flamm) New Database connection feature (iHOP)

CellDesigner2.5 supports simulation and parameter scan by an
integration with SBML ODE Solver. Once you have installed
CellDesigner2.5, you can browse and modify existing SBML models, simulate and view the dynamics through an intuitive graphical interface. The graphical notation scheme used in CellDesigner is based on a proposal by Kitano, et al. ("Using process diagrams for the graphical representation of biological networks",Nature Biotechnology  23(8), 961 - 966 (2005)).
By using CellDesigner, you can create your model with references to existing databases, simulate and analyze the dynamics.

for details:check celldesigner.org

Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System (Fedora Core 4 or later) >>Install Instructions

Features:
CellDesigner 3.0 alpha release is a preview version of umcoming formal release. The intention of this preview release is to provide you with a feel of a new notation that enhanced previous process diagram into gene and RNA, as well as protein complex structure.





Please note that functions of this preview versiion is substantially restricted as the sole purpose of the alpha release is to show the new notation. Version 3.0 implements most part of notations described in Kitano, et al., "Using Process Diagram for Graphical Representation of Biochemical Networks", Nature Biotechnology, August 2005.

For any serious work, please use on-going version CellDesigner 2.2 (or 2.5 which will be released shortly).

Note: you can NOT SAVE YOUR MODEL with this version.
You can open and edit your SBML model (which includes a model created by CellDesigner 2.x). You can also export your model to image file (JPEG, PNG, SVG) for your publication, CSV and pure SBML file for simulation. The exported pure SBML file doesn't contain graphical information, but other information such as kinetic laws, parameters, initial concentrations etc. are stored.

Operating Environment:

Windows (98 or later) MacOSX (10.3 or later) Linux with X Window System >>Install Instructions

Features:

Connection to Databases (PubMed,DBGET,SGD) Export Images to SVG

for details:check celldesigner.org


Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System >>Install Instructions

Features:
This is the bug fix version of 2.1.
-"Export List to CSV" now fixed.





Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System *Note*:For Windows users, download SBW_1_modules from CellDesigner 2.1 section to activate SBW simulators >> Install Instructions

Features:

SBW 2.0 Support Install made easy Bug fixes

CellDesigner2.5 supports simulation and parameter scan by an integration with SBML ODE Solver. Once you have installed CellDesigner2.5, you can browse and modify existing SBML models,simulate and view the dynamics through an intuitive graphical interface. The graphical notation scheme used in CellDesigner is based on a proposal by Kitano, et al.("Using process diagrams for the graphical representation of biological networks",Nature Biotechnology 23(8), 961 - 966 (2005)) By using CellDesigner, you can create your model with references to existing databases, simulate and analyze the dynamics.

for details:check celldesigner.org

Operating Environment:

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System

*Note*:For Windows users, download SBW_1_modules to activate SBW simulators
>> Install Instructions

Features:
* Intuitive User Interface
* Display Species and Compartments in color
* Extensive Notes Description (to Compartment, Species, Reaction, Protein)




* Support New Symbols
  - Relationship between elements: unknown catalysis, unknown inhibition.
  - Residue Modification: Hydroxlated
* Block Diagram support
  - Extract the control relationship between Proteins from the pathway diagram.
  - Describe and Verify the Modifications/Activations Logic.
* SBML Level-2 and Level-1 Compliant
* Export Lists to CSV format
* Export diagram to PNG format

Operating Environment:
CellDesigner 2.0 beta requires Java2 Runtime Environment (JRE1.4.2 or later) on

Windows (98SE or later) MacOSX (10.3 or later + Java 1.4.2_05 or later) Linux with X Window System *Note:If you are interested in time evolving simulation and analysis on biochemical networks, we recommend you to install the Systems Biology Workbench (SBW) 1.0.5 and SBW-powered softwares before you install CellDesigner.

Features:
* Read/write models in SBML Level 1 (version 1) format
* Drawing state transition diagram of proteins
* Detailed expression of modifications of proteins
* Simulations using SBW simulator modules



Operating Environment:
The current version of CellDesigner requires Java2 Runtime Environment (JRE1.3.x) on Windows (98SE or later), MacOS X, and Linux with X Window System.

Please feel free to contact CellDesigner Development Team (celldesigner@systems-biology.org) for any questions or bug reports.