Result: Cell Illustrator 4.0: a computational platform for systems biology.

Title:
Cell Illustrator 4.0: a computational platform for systems biology.
Authors:
Nagasaki M; Human Genome Center, Institute of Medical Science, University of Tokyo, Japan. masao@ims.u-tokyo.ac.jp, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S
Source:
In silico biology [In Silico Biol] 2010; Vol. 10 (1), pp. 5-26.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: SAGE Publications Country of Publication: Netherlands NLM ID: 9815902 Publication Model: Print Cited Medium: Internet ISSN: 1434-3207 (Electronic) Linking ISSN: 13866338 NLM ISO Abbreviation: In Silico Biol Subsets: MEDLINE
Imprint Name(s):
Publication: 2025- : [Thousand Oaks, CA] : SAGE Publications
Original Publication: Amsterdam ; Washington, DC : [Tokyo] : IOS Press ; Ohmsha, c1998-
MeSH Terms:
Computer Simulation* , Models, Biological* , Programming Languages* , Systems Biology* , User-Computer Interface*, Animals ; Base Sequence ; Cell Physiological Phenomena ; Humans ; Internet ; Metabolic Networks and Pathways ; Software ; Transcription, Genetic
Entry Date(s):
Date Created: 20120321 Date Completed: 20130910 Latest Revision: 20161125
Update Code:
20250114
DOI:
10.3233/ISB-2010-0415
PMID:
22430219
Database:
MEDLINE

Further Information

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.