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Cell Illustrator - CI Projects


University of Tokyo is developing Cell Illustrator to support the company's own research efforts as well as research collaborations with other pharmaceutical companies.

Cell Illustrator is based on Genomic Object Net (GON), a previous project at Miyano Lab, Human Genome Center, University of Tokyo. GON was also extensively used in Matsuno lab in Yamaguchi University and succeeded to model various biological pathways.

Launched in 2002, Cell Illustrator runs on all platforms including Windows, Mac OS X, and Linux, and enables biologists to visually analyze biological pathways. Also provided with the software is a gene network data sample, based on baker's yeast.

A tested industrial-quality software system, Cell Illustrator is also already in use by the Institute for Molecular Bioscience and the ARC Center in Bioinformatics' Visible CellTR project at the University of Queensland in Australia.

The internal biological pathway format of Cell Illustrator is Cell System Markup Language. The specification, tools and various models with CSML format are maintained in the CSML website of Human Genome Center, University of Tokyo. You can find very useful information, e.g. examples of biological pathway models (also for download), instructions and screenshots. Yamaguchi University also compiles fruitful information of biological pathway models with Cell Illustrator.

University of Tokyo was the first organization in the world to succeed in large-scale mapping of human gene regulatory networks. Data on the results of this research is available on the Cell Illustrator with options.




”… a highly valuable tool in helping to advance the research efforts undertaken here for the Visible CellTR project. It is a goal of the Visible CellTM project to map the output of Cell Illustrator onto a 3D physical model of the cell so that network models can be integrated and visualized …” said Professor Mark Ragan, the University of Queensland.


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.

This is a list of projects that are related to Cell Illustrator. This list is not a comprehensive survey of these projects. Feel free to contact us, if you have any comments regarding this page.

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