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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 AnimatorTM.
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- 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
CI Project
Cell Illustrator has been developed originally at the Human Genome Center, University of Tokyo in cooperation with the Yamaguchi University. The commercialized version is now sold from Gene Networks International (GNI).
Both universities maintain special webpages that are dedicated to Cell Illustrator. Here you can find very useful information, e. g. examples of biopathway models (also for download), instructions and screenshots.
System requirements
To work correctly, Cell Illustrator requires Java Runtime Environment (JRE) 1.5.0 or higher.
For Linux and Windows platforms, you have an option to download the installer with or without JRE.
Cell Illustrator v3.0 is available for the following platforms:
- Windows NT/2000/XP without Java (size 66MB)
- Windows NT/2000/XP with Java (size 90MB)
- Unix (size 54MB)
- Linux without Java (size 54MB)
- Linux with Java (size 85MB)
- Mac OS X (size 63MB)
Hardware
- Recommended
CPU: > 2 GHz
RAM: 512 MB
- Minimum
CPU: > 1 GHz
RAM: 256 MB
Disk space: 100 MB
Cell Illustrator Server
- Operating System
- Linux
- Windows
- any other OS with Java 1.5, Apache Tomcat and Apache Axis
- Web Server
- Apache Tomcat version 5.0 or higher
- Apache Axis version 1.2RC3
- Java SDK compatible with Apache Axis
- Simulation Engine
- Java Runtime Environment, JRE version 1.5.0 or higher
Recommended Hardware
Pentium® IV processor - 2 GHz or faster
512 MB RAM or more
1 GB available hard disk space |
