Cell Illustrator Pro v3.0 01.30.2007

Cell Illustrator Pro v3.0 01.30.2007
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Cell Illustrator Pro v3.
Windows + MACOSX + Linux

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

Cell Illustrator models are used to visualize biopathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts.

Cell Illustrator provides biochemists with comprehensive visual representations of biochemical processes which form large and complex networks. The software gives new insight to understanding these networks and relationships between chemical components in structurally complex dynamic interactions and processes.

Cell Illustrator aids researchers in modeling metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

Cell Illustrator has been successfully used to model: gene regulation of the lac operon, Circadian Rhythms in Drosophila melanogaster, Apoptosis Induced by Fas ligand, and the switching mechanism of λ phage.

Easy-to-use Petri Net design methodology and intuitive interface make the Cell Illustrator software an excellent tool for biologist, biochemists, and scientists conducting research in life sciences as well as for graduate educators.

Using Cell Illustration requires no advanced knowledge of differential equations and/or higher mathematics.

Biological pathways modeled with the Cell Illustrator can be visualized and animated using Cell Animator™.

Key Features

* Easy and intuitive User Interface
* SVG Library of biological elements
* All model’s variables and parameters of processes and connectors are tabulated and are easy to modify
* Variables’ actual values can be displayed during simulation
* Five simulation modes: three different continuous simulation modes, step simulation and step simulation with animation
* Discrete processes have unique animated simulation option to observe quantities flow through the system
* Simulation results can be presented on real-time graphs or exported to common format files
* A simulation run can be saved in a log file and replayed in Cell Illustrator Player
* The Simulation History dialog provides access to previous versions of a model and simulation results
* Final simulation results can be presented using Cell Animator with graphs and animations. Sample verified biochemical models created using Cell Illustrator are available
* Import of SBML and CellML models
* Special visualization mode dedicated for the analysis of Gene Relationship Networks

Cell Illustrator can be used for:
Easy construction and visualization of biological pathways and processes
Simulation of systems that include both discrete and continuous processes
Simulation animation
Creating model diagrams of publication quality
Importing models from public or proprietary libraries and databases like KEGG
Analysis and exploration of gene relationship networks

New in This Release 3.0 (latest version)

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.

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