News
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.
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.
January 16, 2008
Masao Nagasaki gave an oral presentaion at the conference of JSBi 2007
Masao Nagasaki gave an oral presentation in English co-authored by Euna Jeong, Kazuko Ueno, Emi Ikeda, Chen Li, Kaname Kojima, Ayumu Saito and Satoru Miyano at The 2007 Annual Conference of Japanese Society for Bioinformatics held at MIRAIKAN, Tokyo Academic Park, December 17, 2007. The presentation is entitled "Cell Illustrator 3.5 and Cell System Ontology 3.0", which proceeded at the session of "Databases and Ontologies". The details could be referred from here =>
Ayumu Saito, Euna Jeong, Chen Li, Kaname Kojima and their collaborators also gave the research outcome at poster sessions. In the meantime, they demonstrated Cell Illustrator 3.5 as well as Cell Illustrator Online 4.0 at software demonstration session of the same conference.
December 25, 2007
An article will appear in an issue of Journal of Wako Pure Chemical Industries, Ltd. (Infomatic World)
Satoru Miyano has written an article in Japanese entitled, "Fusion of modeling and simulation with experimental data for biological systems - Let's introduce a strategic IT tool of systems biology into your research".
This article will appear in the issue of Journal of Wako Pure Chemical Industries, Ltd. (Infomatic World) from which you can thoroughly understand the current situation of systems biology and future development of Cell Illustrator.
Interesting? Click here to read the original text in PDF format
November 9, 2007
Poster presentation in the 7th International Workshop on Advanced Genomics New Horizon
The 7th International Workshop on Advanced Genomics New Horizon will be held at Tokyo International Forum, JP, on 27-28 November, 2007. This workshop aims to provide researchers from various fileds with the opportunity to communicate, exchange and share their newest views and ideas. The conference plans to cover rapidly expanding new frontiers of genomics including "Application of New Sequencing Technology", "Metagenomics", "The Role of Non-coding RNA", "Bioinformatics", "Personalized Medicine / Pharmacogenomics", and "Chemogenomics".
The research presentation "Cell System Markup Language 3.0 and its Platform Cell Illustrator 4.0 for Systematic Translation of Cell System" will be given by Dr. Jeong and Dr. Li at poster session, which focus on the development of a new XML format Cell System Markup Language (CSML) and its execution environment Cell Illustrator 4.0 to translate the systematic behaviors in living organisms. Link to the website about workshop =>
October 24, 2007
Genome Square 2007 in Osaka
Genome Square 2007 was successfully held in Osaka, Oct. 13-14, 2007, which was organized by the Ministry of Education, Culture, Sports, Science and Technology specific area research. About 200 genome researchers explained their research together with actual living organisms, DNA, experimental machine and computers in an easy-to-understand manner.
Dr. Saito and Mr. Kojima from Miyano Lab. gave the explaination and answered the questions and doubts in this event. The title is "Launched an attention to the Life Simulation from high school - From genome to metabolism". Followings are the related documents, please refer to the number of "A2".
In addition, the lower right picture is the group photo of Miyano Lab. taken last month, which was posted on the Abstract of Genome Square 2007 Introduction booklet.
October 19, 2007
Poster presentation in Life Science Research Network Symposium 2007
The Life Science Research Network Symposium 2007 was held at Yasuda Hall, University of Tokyo, 15th Sep. 2007. It was also organized as an event of 130th anniversary for University of Tokyo FOUNDATION.
Dr. Nagasaki gave a presentation at Poster session with the title of "Ontology language CSML and its implementation to Cell Illustrator 3.5 to systematically translate life phenomena". This research project is also contributed by E. Jeong, K. Ueno, E. Ikeda, K. Kojima, A. Saito and S. Miyano. Now their poster and the format for distribution are available as PNG files.
August 10, 2007
Poster presentation in ISMB/ECCB 2007
The 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) held along with the 6th European Conference on Computational Biology (ECCB) was held at the Austria Center Vienna in Vienna, Austria in July 21-25, 2007. The research presentation "Cell System Markup Language CSML 3.0 Enhanced with System Dynamics Ontology and Its Application to Cell Illustrator 3.5" was given by Satoru Miyano at Poster session (Poster C073).
May 31, 2007
CI Book (Japanese) has been published in July, 2007
The book "What does Systems Biology do? - Let's start with Cell Illustrator-" written by A. Doi, M. Nagasaki, A. Saito, H. Matsuno, S. Miyano has been published by Kyoritsu Shuppan Co., Ltd. on July 15th, 2007. It is available now on Amazon.co.jp.
May 9, 2007
Cell Illustrator 3.0 are released
In March 2007, we released the new version of Cell Illustator. The new release is version 3.0, and it contains CSML.
Cell Illustrator 3.0 is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover it allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.
Cell Illustrator 3.0 models are used to visualize biological pathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts. See http://www.cellillustrator.com for details.
January 25, 2007
Poster presentation in PSB2007
In early January, We announced the CSML world in PSB2007--Pacific symposium on biocomputing. The poster is now available. >> show image
December 14, 2006
CSML1.9.1 format and its parser are released
The CSML1.9.1 format and its libraries are released. In CSML1.9.1, the previous CSML1.9 format is slightly extended to handle some major classes in Cell System Ontology 3.0. The format is used in Cell Illustrator 3.0. At the same time, LGPL licensed library with Java language is released. The online viewer of the API is also available.
