Cell Illustrator 3.0

Import of SBML/CellML files:
New input filters allow importing models stored in the widely used CellML and SBML formats. The imported SBML/CellML models are converted to Cell Illustrator models and can be edited, analyzed, simulated or saved as any other Cell Illustrator model. This function converts SBML/CellML models, which use differential equations for representing relationships between entities, to CI models, which use the Petri Net formalism used in CI.

Library of SVG graphical elements:
The library of Biological Elements has been extended with SVG images representing biological entities, processes and cellular components. The library consists of: about 40 images for biological entities, more than 250 images for biological processes and about 70 images for cell components. Each image corresponds to one Gene Ontology (or Cell System Ontology) term. Each image can be edited in the SVG editor included in Cell Illustrator.

Enhancements in the Petri Net simulation engine:
New options for a better control of the simulation flow have been added. The weak firing and firing accuracy options available in the Simulation Settings facilitate the simulation of continuous models.

Improved Charts:
Charts dialog boxes have been enhanced for improved viewing, analysis and control of simulation results.

External References:
Since the version 3.0, Cell Illustrator offers an extensive support for external references to public databases, Gene or Cell Ontology terms, etc. These references can be defined in the new Biological tab of the Element Setting dialog box, as well as in the redesigned External References dialog box. Also, URL Templates can be defined to access public databases. The URLs of the external references can be opened in the web browser.

Gene Network View:
The added Gene Network Mode enables the user to view and explore gene relationships networks. This mode offers a special visualization style and tools for the analysis of gene relationship networks, such as Pathway Search, Sub-network Extraction and Network Merge.