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Volume 10


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In Silico Biology 10, 0002 (2010); ©2009, Bioinformation Systems e.V.  



Cell Illustrator 4.0: A computational platform for systems biology

Masao Nagasaki*, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda and Satoru Miyano

Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan

* Corresponding author
   Email: masao@ims.u-tokyo.ac.jp


Edited by E. Wingender; received October 05, 2009; revised December 22, 2009; accepted December 25, 2009; published January 09, 2010


Abstract

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.


Keywords: biopathway, simulation, Petri net, modeling, pathway database, ontology, CSML, CSO, CI, ODE, Cell Illustrator, Java, JWS