Overview
The Cell System Markup Language (CSML) is an XML format for modeling, visualizing and simulating biopathways. CSML supports to represent several pathway types including metabolic, signaling, and genetic regulatory pathways.
This project aims to facilitate the exchange of biopathway data in different formats. Effort has been made for data conversion from other XML formats. In addition, to allow extensible and flexible features of CSML, the Cell System Ontology (CSO) has been developed.
News
2010年01月26日
New Jounal Paper Published in In Silico Biology
Our new paper "Cell Illustrator 4.0: A computational platform for systems biology" co-authored by Masao Nagasaki, Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima, Emi Ikeda and Satoru Miyano
has been formally accepted and published in the "Special Issue: Petri Net Applications in Molecular Biology" of In Silico Biology in January 2010.
The paper can now be freely accessed on the In Silico Biology Website.
The paper's citation is Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S, Cell Illustrator 4.0: A computational platform for systems biology, In Silico Biol., 10, 0002, 2010.
To read the paper, please click here.
2009年12月22日
Mini-Genome Square 2009 in Fukuoka, Japan
Li, Saito, Fujita, and Chalkidis attended the event "Mini-Genome Square 2009" at ELGALA Hall, in Fukuoka, December 20, 2009, which was organized by the Ministry of Education, Culture, Sports, Science and Technology specific area research. Many visitors have participated this event. The genome researchers explained their research together with actual living organisms, DNA, experimental machine and computers in an easy-to-understand manner.
We gave the explanation and answered the questions and doubts in this event. The title is "To understand bio-simulation from spot different game - health and disease".
2009年08月05日
Genome Square 2009 in Akihabara, Japan
Genome Square 2009 was successfully held at Akiba Square, August 01-02, 2009, which was organized by the Ministry of Education, Culture, Sports, Science and Technology specific area research. Over 1000 visitors have participated this event. The genome researchers explained their research together with actual living organisms, DNA, experimental machine and computers in an easy-to-understand manner.
Li, Saito and Koh from Miyano Lab gave the explanation and answered the questions and doubts in this event. The title is "To understand bio-simulation from spot different game - health and disease".
In the right picture, Li was introducing Cell Illustrator Online to some undergraduate students.
Poster in PDF format| Poster in PNG format (light version)
2009年06月25日
Oral talk in the 10th BioPathways Meeting in Stockholm (ISMB/ECCB 2009)
Oral talk Cell Illustrator Online: A Computational Platform for Systems Biology will be presented in the satellite meeting BioPathways of ISMB/ECCB 2009 on 27/Jun/2009.
2009年05月15日
New Jounal Paper Published in BMC Systems Biology
Our new paper "Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension" written by Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano has been formally accepted and published by BMC Systems Biology in 27 April 2009.
The preliminary form of the paper now can be freely accessed on the BMC Systems Biology Website.
The paper's citation is C. Li*, M. Nagasaki*, K. Ueno and S. Miyano, Simulation-based Model Checking Approach to Cell Fate Determination During Caenorhabditis elegans Vulval Development by Hybrid Functional Petri Net with Extension, BMC Syst Biol., 3:42, 2009 Apr. (*These authors equally contributed to this work).
To read and download the paper, please click here.
Supplemental DATA including CSML models, simulation results, source code and the PPT file underlying the framework of this research are freely available here.
About the CSML project
The CSML project is a collaboration between Human Genome Center and Biopathway Analysis Center.
