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.
September 11, 2008
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
June 24, 2008
Paper accepted for publication in BMC Systems Biology
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.
June 5, 2008
Research Result Symposium 2008 in the Institute of Medical Science
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.
May 28, 2008
News Announcement of CIO Release on SBML.org
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.
May 13, 2008
Cell Illustrator Online 4.0 with CSML + BIOBASE TRANTHPATH
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.
