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*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.

Models created by CellDesigner:
EGFR Pathway Map, Molecular Interaction of Macrophage, PANTHER Classification System, Check Model Repositories section under Resources for more.

CellDesigner 4.4 (2014/07/12)

Features:

ChEBI Database connection support + SBGN-ML Plugin API + library updates (libSBGN-ML + SimulationCore) + connection updates (DBGET + SABIO-RK)  + bug fixes.

Operating Environment:

cd44.pngのサムネール画像
  • Windows 32bit. 64bit
  • MacOSX (10.6 or later)  32bit. 64bit
  • Linux with X Window System (Fedora Core 4 or later)  32bit. 64bit

  • >>Install Instructions


    posted 2014.07.12

    CellDesigner 4.3 (2013/02/01)

    Features:

    CellDesigner 4.3 supports libSedML + libSBGN-ML + SABIO-RK reaction information import function update + bug fixes.

    CD43Sabio-rk_120.png Operating Environment:

  • Windows (XP or later) 32bit only
  • MacOSX (10.6 or later) 
  • Linux with X Window System (Fedora Core 4 or later)

  • >>Install Instructions

    posted 2013.02.01

    CellDesigner 4.2 (2011.10.5)

    ControlPanel42_sc2_120.pngFeatures:
    CellDesigner 4.2 supports Reduced Notation + Simulation Parameter Polymorphism, and SBMLsim solver.


    reducednotation_th.pngOperating Environment:

  • Windows (XP or later) 32bit only
  • MacOSX (10.5 or later)
  • Linux with X Window System (Fedora Core 4 or later)

  • >>Install Instructions


    posted 2011.10.05

    CellDesigner 4.1 (2010.06.30)

    Features:
    CellDesigner 4.1 supports SBML Level 2 Version 4, enabling MIRIAM annotation, export to BioPAX level 3 and SABIO-RK integration.

    Operating Environment:
  • Windows (XP or later)
  • MacOSX (10.5 or later)
  • Linux with X Window System (Fedora Core 4 or later)

  • >>Install Instructions

    posted 2010.06.30

    CellDesigner 4.1 beta (2009.8.28)

    Features:
    CellDesigner 4.1 beta supports SBML Level 2 Version 4, enabling MIRIAM annotation, and SABIO-RK integration.

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

  • >>Install Instructions

    posted 2009.08.26

    CellDesigner 4.0.1 (2008.8.12)

    components40_120.png Features:
    CellDesigner 4.0.1 is the bug fix version of CellDesigner 4.0. Ver.4.0 enhances Graphical Notation, based on SBGN Level 1 proposal.




    KineticLaw_edit_250.png * If you create/edit a file with this new version, your model will not be able to open with the lower version of CellDesigner.
    Please check the file compatibilities.

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

  • >>Install Instructions

    Bug Fixes
    - Notes data may be lost when saving the file.
    - SBW connection: CellDesigner annotation data is not passed to SBW modules.
    - Database link to Genome Network Platform is not working
    - Incorrect error messages for simulation.
    - Cannot set stoichiometry value other than 1

    posted 2008.08.13

    CellDesigner 4.0 (2008.8.4)

    components40_120.png Features:
    CellDesigner 4.0 is the enhanced Graphical Notation version, based on SBGN Level 1 proposal. Other new features and updates in CellDesigner 4.0.




    KineticLaw_edit_250.png * If you create/edit a file with this new version, your model will not be able to open with the lower version of CellDesigner.
    Please check the file compatibilities.

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

  • >>Install Instructions

    NOTICE: (2008/08/08) We have found serious bugs in CellDesigner4.0, and we are preparing the bug fix version now. We would strongly recommend you to wait for the bug fix version 4.0.1. If you want to try 4.0 features, please be aware of the following bugs.

    - Notes data may be lost when saving the file.
    - SBW connection: CellDesigner annotation data is not passed to SBW modules.
    - Database link to Genome Network Platform is not working
    - Incorrect error messages for simulation.

    posted 2008.08.01

    CellDesigner 4.0beta for Graphical Notation Preview (2007.12.7)

    20071207_a.jpgFeatures:
    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.




    20071207_b.gif* 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


    posted 2007.12.07

    CellDesigner 3.5.2 (2007.11.15)

    20071115_a.gifFeatures:
    CellDesigner3.5.2 is the bug fix version of CellDesigner 3.5.1.





    20071115_b.gifOperating 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

    posted 2007.11.15

    CellDesigner 3.5.1 (2007.1.10)

    20070110_a.gifFeatures:
    CellDesigner3.5.1 is the bug fix version of CellDesigner 3.5.






    20070110_b.gifOperating 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


    posted 2007.01.10

    CellDesigner 3.5 (2006.12.28)

    20061228_a.jpgFeatures:
    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.




    20061228_b.gifOperating 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

    posted 2006.12.28

    CellDesigner 4.0alpha for Plugin Developer's Preview (2006.10.7)

    20061007_a.gifFeatures:
    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.


    20061007_b.gifOperating 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


    posted 2006.10.07

    CellDesigner 3.2 (2006.7.5)

    20060705_a.gifFeatures:
    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.




    20060705_b.gifOperating 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

    posted 2006.07.05

    CellDesigner 3.1 (2006.3.24)

    20060324_a.gifFeatures:
    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.


    20060324_b.gifOperating 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

    posted 2006.03.24

    CellDesigner 3.0.1 (2006.1.26)

    20060126_a.jpgFeatures:
    CellDesigner3.0.1 is the bug fix version of CellDesigner 3.0.





    20060126_b.gifOperating 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


    posted 2006.01.26

    CellDesigner 3.0 (2005.10.15)

    20051015_a.gifFeatures:
    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.


    20051015_b.gifCellDesigner3.0 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


    posted 2005.10.15

    CellDesigner 2.5 (Released 2005.9.1)

    20050901_a.gifFeatures:
  • Simulation and parameter scan feature by an integration
       with SBML ODE Solver (Thanks to Rainer Machne and Christoph Flamm)

  • New Database connection feature (iHOP)


  • 20050901_b.gifCellDesigner2.5 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


    posted 2005.09.01

    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.



    20050804_b.gif

    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


    posted 2005.08.04

    CellDesigner 2.2 (Released 2005.5.24)

    20050524_a.jpgFeatures:
  • Connection to Databases (PubMed,DBGET,SGD)

  • Export Images to SVG

  • for details:check celldesigner.org


    20050524_b.jpg 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

    posted 2005.05.24

    CellDesigner 2.1.1 (Released 2005.1.18)

    20050118_a.jpgFeatures:
    This is the bug fix version of 2.1.
    -"Export List to CSV" now fixed.





    20050118_b.jpgOperating 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

    posted 2005.01.18

    CellDesigner 2.1 (Released 2005.1.12)

    20050112_a.jpgFeatures:
  • SBW 2.0 Support

  • Install made easy

  • Bug fixes



  • 20050112_b.jpgCellDesigner2.5 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

    posted 2005.01.12

    CellDesigner 2.0 (Released 2004.9.30)

    20040930_a.pngFeatures:
    * Intuitive User Interface
    * Display Species and Compartments in color
    * Extensive Notes Description (to Compartment, Species, Reaction, Protein)




    20040930_b.png* 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.


    posted 2004.09.30

    CellDesigner 2.0 beta (Released 2004.8.26)

    20040826_a.png
    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.


    20040826_b.png* 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.

    posted 2004.08.26

    CellDesigner 1.1 (Released 2003.10.28)

    20031028_a.gif
    Features:
    * Identification of species in different compartments
    * Read/write models in SBML Level 1 (version 2) format
    * Drawing state transition diagram of proteins
    * Detailed expression of modifications of proteins
    * Simulations using SBW simulator modules
    * For detail see Changes


    20031028_b.gifOperating Environment:
    CellDesigner 1.1 requires Java2 Runtime Environment (JRE1.3.x) on Windows (98SE or later), MacOS X, and Linux with X Window System.

    posted 2003.10.28

    CellDesigner 1.0 (Released 2003.6.9)

    20030609_a.gifFeatures:
    * 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



    20030609_b.gifOperating 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.

    posted 2003.06.09