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 at a glance

APBC2011 and the paper published in BMC Bioinformatics


The Ninth Asia-Pacific Bioinformatics Conference, APBC2011, was held in Incheon, Korea (Jan. 11-14, 2011). Euna Jeong has presented the research paper "Ontology-based instance data validation for high-quality curated biological pathways, by Euna Jeong*, Masao Nagasaki*, Kazuko Ueno, and Satoru Miyano (*equal contributor)," which will be published in BMC Bioinformatics on February 15, 2011.

The oral presentation is available at the Biological Research Information Center (BRIC).

MIRACH 1.0 paper published - January 2011


The paper "MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models." by Hock Koh C, Nagasaki M, Saito A, Li C, Wong L, Miyano S is published by Oxford Journals' Bioinforamtics in the Bioinformatics Advance Access on January 5, 2011. MIRACH is our efficient Model checker for verifying specified properties of biological pathway models. You can find the abstract and full text here...

Cell Illustrator book (Korean version) has been published on Nov. 20, 2010


Happy New Year!

The Korean version of our book "What does Systems Biology do? - Let's start with Cell Illustrator-" translated by Jin Hwan Do and Euna Jeong has been published on November 20, 2010.

Click here to see the Product Details of the book in Korean.

Contributions to the new book


Ayumu Saito, Masao Nagasaki from Miyano lab and Prof. Matsuno from Yamaguchi University, have contributed to write the chapter of the new book "Modeling in Systems Biology". The book will be published on October 22, 2010 by Springer.

They have written the part entitled "Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling" in Part II: Modeling Techniques.

The book can be accessed from this website and Amazon.

Prof. Chaouiya visited Miyano Lab


Prof. Claudine Chaouiya first visited Miyano Lab in Sep. 9, 2010. We discussed about the application of Petri net to the field of Systems biology. Prof. Chaouiya gave the presentation about her group's recent research, for example, the analysis by using logical model, model checking and so on.

Prof. Chaouiya and Chen Li are the members of Program Committee of the Workshop on Biological Processes and Petri Nets (BioPPN2011). BioPPN2011 is the satellite workshop of PETRI NET 2011 and ASCD 2011, which will be held in June 20-24, 2010, Kanazawa, Japan. We encourage submissions of your inspired contributions relating to all aspects of the application and theory of Petri nets to Systems biology. Program of BioPPN2010 can be accessed from the website for your consideration.

Click HERE to visit Prof. Claudine Chaouiya's Homepage.

The official HP of PETRI NET 2011 and ASCD 2011.

Poster presentation in ISMB2010@Boston


The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010) was successfully taken place at the John B. Hynes Convention Center in Boston, MA, USA in July 11-13, 2010. Chen Li has attended the conference and gave the research presentation "Time-dependent key element analysis with active state transition diagram: a high-level Petri net approach" at Poster session (Poster X072). This poster is an introduction of our recent paper published in BMC Systems Biology.

Link to the website for the long abstract =>

Show poster image =>

Paper accepted for publication by BMC Systems Biology


Our new paper "Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram" written by Chen Li, Masao Nagasaki, Ayumu Saito, Satoru Miyano has been formally accepted and published by BMC Systems Biology in 1 April 2010. The preliminary form of the paper now can be freely accessed on the BMC Systems Biology Website.

The citation of this paper is C. Li*, M. Nagasaki*, A. Saito and S. Miyano, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, BMC Syst Biol., 4:39, 2010 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.

The Second NUS-UT Workshop on Computational Systems Biology in Tokyo


The Second NUS-UT Workshop on Computational Systems Biology was successfully held at the Institute of Medical Science, University of Tokyo, February 22-23, 2010.

This is a bilateral workshop between National University of Singapore (NUS) and University of Tokyo (UT). Prof. Thiagarajan from NUS gave the plenary lecture with the title "Computational and Verification Platforms for Systems Biology" on the first day. Dr. Shibuya gave the other one about Next-Generation Cancer Genome Analysis Pipeline on the next day.

Please click here to see the contents of program and abstracts.

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.

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".

About the CSML project

The CSML project is a collaboration between Human Genome Center and Biopathway Analysis Center.