Cell Illustrator 4.0: A Computational Platform for Systems Biology
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 capabi...
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| Published in | In silico biology Vol. 10; no. 1-2; pp. 5 - 26 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London, England
SAGE Publications
2010
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1386-6338 1434-3207 1434-3207 |
| DOI | 10.3233/ISB-2010-0415 |
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| 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. |
|---|---|
| AbstractList | 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. 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.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. 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. |
| Author | Li, Chen Miyano, Satoru Saito, Ayumu Kojima, Kaname Nagasaki, Masao Jeong, Euna Ikeda, Emi |
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| Snippet | 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... 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... |
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| SubjectTerms | Animals Base Sequence Cell Physiological Phenomena Computer Simulation Humans Internet Metabolic Networks and Pathways Models, Biological Programming Languages Software Systems Biology Transcription, Genetic User-Computer Interface |
| Title | Cell Illustrator 4.0: A Computational Platform for Systems Biology |
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