| CellDesigner |
CellDesignerTM is a modeling tool of biochemical networks with graphical user interface. It is designed to be SBW (Systems Biology Workbench) compliant, and support SBML (Systems Biology Markup Language) format.
Quick View of CellDesigner
Models created by CellDesigner:
[EGFR Pathway Map], [Molecular Interaction of Macrophage]
[PANTHER Classification System] Check Model Repository Section for more. |
| Release Name: CellDesigner 4.0beta for Graphical Notation Preview (2007.12.7) |
| 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
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| Download for Windows>> |
| Download for Mac OSX (10.4.x)>> |
| Download for Linux>> |
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| Release Name: CellDesigner 3.5.2 (2007.11.15) |
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| Release Name: CellDesigner 3.5.1 (2007.1.10) |
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| Release Name: CellDesigner 3.5 (2006.12.28) |
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| Release Name: CellDesigner 4.0alpha for Plugin Developer's Preview (2006.10.7) |
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| Release Name: CellDesigner 3.2 (2006.7.5) |
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| Release Name: CellDesigner 3.1 (2006.3.24) |
| 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
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| Download for Windows>> |
| Download for Mac>> |
| Download for Linux>> |
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| Release Name: CellDesigner 3.0.1 (2006.1.26) |
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| Release Name: CellDesigner 3.0 (2005.10.15) |
| 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
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| Download for Windows>> |
| Download for Mac>> |
| Download for Linux>> |
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| Release Name: CellDesigner 2.5 (Released 2005.9.1) |
| 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
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| Download for Windows>> |
| Download for Mac>> |
| Download for Linux>> |
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| Release Name: CellDesigner ver3.0 alpha for Graphical Notation Preview (Released 2005.8.4) |
| 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
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| Download for Windows>> |
| Download for Mac>> |
| Download for Linux>> |
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| Release Name: CellDesigner 2.2 (Released 2005.5.24) |
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| Release Name: CellDesigner 2.1.1 (Released 2005.1.18) |
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| Release Name: CellDesigner 2.1 (Released 2005.1.12) |
| 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
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| Download for Windows>> |
| Download SBW 1 Modules>> |
| Download for Mac>> |
| Download for Linux>> |
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| Release Name: CellDesigner 2.0 (Released 2004.9.30) |
| 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.
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| Download for Windows>> |
| Download for MacOSX>> |
| Download for Linux>> |
| Startup Guide>> |
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| Release Name: CellDesigner 2.0 beta (Released 2004.8.26) |
| Features: | * Intuitive User Interface
* Display Species and Compartments in color
* Block Diagram support
- Extract the control relationship between Proteins from the pathway diagram.
- Describe and Verify the Modifications/Activations Logic.
* Extensive Notes Description (to Compartment, Species, Reaction, Protein)
* Support New Symbols
- Relationship between elements: unknown catalysis, unknown inhibition.
- Residue Modification: Hydroxlated
* 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), and Linux with X Window System.
Please feel free to contact CellDesigner Development Team (celldesigner @ systems-biology.org) for any questions or bug reports.
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| Download for MacOS X>> |
| Download for Windows>> |
| Download Startup Guide(pdf)>> |
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| Release Name: CellDesigner 1.1 (Released 2003.10.28) |
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| Release Name: CellDesigner 1.0 (Released 2003.6.9) |
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