Cell System Markup Language (CSML)

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"

2008年09月11日

Genome Square 2008 in Nagoya, Japan

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