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 =>

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 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.

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.

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".

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)

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.

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.

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.

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"

Genome Square 2008 was successfully held at Nagoya University, Oct. 25-26, 2008, which was organized by the Ministry of Education, Culture, Sports, Science and Technology specific area research. This is the first time to held such symposium in Nagoya. 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.

Saito and Li from Miyano Lab. gave the explaination and answered the questions and doubts in this event. The title is "To understand a construction principle of life systems in a game-like manner - Let's assemble the blueprint of the life".

In addition, the lower right picture is the photo of our demonstration booth.

Abstract in Japanese| Full poster image

The paper "Systematic reconstruction of TRANSPATH data into Cell System Markup Language" by Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong and Satoru Miyano has been formally accepted in BMC Systems Biology, and has been published in preliminary form on their website in 23 June, 2008.

The article's citation is BMC Systems Biology 2008, 2:53.

To read and download our BMC Systems Biology paper, please click here.

Research Result Symposium 2008 of the Institute of Medical Science was successfully held in in the Institute of Medical Science, May 29-30, 2008, which was organized by the Institute of Medical Science, the University of Tokyo.

Masao Nagasaki gave a short presentation entitled "A tool for system biology: Cell Illustrator Online 4.0" at the session of Flash talk. Masao Nagasaki, Ayumu Saito, Chen Li and Kaname Kojima gave the explanation at the Poster session. Two application research of Cell Illustrator Online 4.0 were also presented by Teppei Shimamura and Mrs. Yamauchi at the same symposium.

SBML.org announced the release news of Cell Illustrator Online 4.0 at "Community News" in the left column on the top page.

Click here for more detailed coverage.

Cell Illustrator Online 4.0 began to offer a service of utilizing the database of BIOBASE TRANTHPATH®.

CSML is applied to act as a bridge to smoothly access the data provided by BIOBASE TRANTHPATH®. In the near future, we will concentrate on accelerating the utilization of CSML and Cell Illustrator Online 4.0 in cooperation with BIOBASE, especially in the development of pathway visualization, experimental data interpretation and pathway simulation.