title: Cell Illustrator 4.0: a computational platform for systems biology.
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.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, Japan. masao@ims.u-tokyo.ac.jp
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Ayumu
authors.initials: A
authors.lastname: Saito
authors.forename: Euna
authors.initials: E
authors.lastname: Jeong
authors.forename: Chen
authors.initials: C
authors.lastname: Li
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.forename: Emi
authors.initials: E
authors.lastname: Ikeda
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000818:Animals; D001483:Base Sequence; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D049490:Systems Biology; D014158:Transcription, Genetic; D014584:User-Computer Interface