Cell illustrator 4.0: A computational platform for systems biology

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

Research output: Contribution to journalArticlepeer-review

57 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)5-26
Number of pages22
JournalIn Silico Biology
Issue number1-2
Publication statusPublished - 2010


  • Biopathway
  • Cell Illustrator
  • CI
  • CSML
  • CSO
  • Java
  • JWS
  • Modeling
  • ODE
  • Ontology
  • Pathway database
  • Petri net
  • Simulation


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