The new Cell Illustrator 5.0 offers new functionality and new features for all researches who wish model, elucidate and simulate complex biological processes and systems.

New features include:
  • New User Interface;
  • Simulation Engine Enhancements;
  • Unified Gene Net and Bio-pathway;
  • Updates in Element Lists,
  • Graph Layout,
  • CSMLDB Search;
  • CSMLPipeline;
  • Curated Executable Macrophage Database;
  • Data Assimilation.
     
Some highlights of the new release:
 
  • New User Interface: The user interface of Cell Illustrator version 5.0 has been rewritten from the scratch in order to facilitate and speed up common operations. The new CI window offers a modern and more intuitive layout including:
    • Docking Frames and Toolbars.
    • Customizable Perspectives and View Settings.
    • Tabbed Pane with Multiple Models.
    • Multiple Views of One Model.
  • Simulation Engine Enhancements: Cell Illustrator 5.0 supports new, more common scripting languages: Java and JavaScript facilitate the definition of complex logic in the Petri Net model, while the dedicated simple-math script language enables very fast execution of pure mathematical formulas. Also other improvements have been done in the simulation mode:
    • Interactive simulation run (e.g. Step mode) for SECG and Reference Simulation.
    • Display of connector/process speed on charts and on the canvas.
    • Easy definition and insertion of Simulation Plug-ins.
    • Simplified creation of simulation logs.
  • Unified Gene Net and Biological Pathway View: The new Fact Edges connecting two entities allow for easier definition of gene networks. Thanks to them the Gene Net mode was integrated with the Bio-Pathway mode into one and the same graph window.
  • Extensive Support for Biological Properties: Handling of Biological Properties was improved by:
    • Support for predefined Cell System Ontology (CSO) classes and hierarchy trees.
    • Improved creating/editing of predefined and user-defined biological properties.
    • Display of all properties in element tables. The new Biological Properties frame allows also for sorting/filtering and finding elements by their biological property values.
    • Display of Chemical Structure on 2D graphs.
    • Display the selected Biological Property on the canvas as element label.
  • Updates in Element Lists, Graph Layout, CSMLDB Search, etc.: Many small enhancements have been done to increase the usability of Cell Illustrator and simplify the creation of CSML models.
    • The CSMLDB Search frame offers the new function of creating user-defined databases from the set of CSML input files, which is available in the new User Database Manager dialog box.
    • The Element Lists offers filtering and sorting of elements by their properties, and dedicated editors to easy the editing of single properties.
    • The Graph Layout frame was reviewed and simplified; all available layout algorithms can be customized using a special Layout Options dialog box.
  • CSMLPipeline: CSMLPipeline is a separate software application created by the University of Tokyo, which allows for transformation and integration of pathway models, gene networks and other biological data basing on the CSML and CSO concepts. CSMLPipeline allows for the automation of often repeated operation flows and procedures.
  • Curated Executable Macrophage Database: The new Curated Executable Macrophage Database can be accessed from a web browser at http://macrophagedb.csml.org. It is based on the CSMLDB concept and allows for searching and browsing pathways, reactions and single molecules within the web browser. Each found pathway can be opened in Cell Illustrator for further analysis or modification.
  • Data Assimilation: The Parameterized Simulation function was extended to facilitate estimation of unknown parameters in a pathway model from time-course information. For a more detailed description and examples of this Data Assimilation procedure please refer to http://da.csml.org/.