Cell Illustrator 4.0: A Computational Platform for Systems Biology

Issue title: Petri Net Applications in Molecular Biology

Article type: Research Article

Authors: Nagasaki, Masao | Saito, Ayumu | Jeong, Euna | Li, Chen | Kojima, Kaname | Ikeda, Emi | Miyano, Satoru

Affiliations: Human Genome Center, Institute of Medical Science, University of Tokyo, Japan

Note: [] Corresponding author. Tel.: +81 5449 5615; Fax: +81 5449 5442; E-mail: [email protected]

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

DOI: 10.3233/ISB-2010-0415

Journal: In Silico Biology, vol. 10, no. 1-2, pp. 5-26, 2010