Cell System Markup Language (CSML)

2010年07月28日

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 =>

2010年04月01日

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.

2010年03月15日

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.

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.

2009年05月15日

CI book (English version) will be published in May 31, 2009

Our new book "Foundations of Systems Biology: Using Cell Illustrator and Pathway Databases (Computational Biology)" written by Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano will be published by Springer on May 31, 2009.

Reading the book using Cell Illustrator bundled in the CD-ROM can make it possible to create highly complex pathways for simulations and analyses. There is no need for prior knowledge in differential equations or programming. The prerequisites are interest in biology, ability to operate a cell phone, and mathematical ability of a standard middle school student or better.

It is now available to browse samples pages HERE at www.amazon.com.

Click here to see the Product Details of the book.

2009年02月20日

INBIOSIS Seminar 02

Miyano, Nagasaki and Saito have attended the workshop held at Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Malaysia, January 20-21, 2009.

Miyano has given a presentation with two themes:

• "Computing Molecular Networks and Dynamics for Systems Biology"
• "Prospect in Computational Biology"