News at a glance

APBC2011 and the paper published in BMC Bioinformatics

bioinformatics

The Ninth Asia-Pacific Bioinformatics Conference, APBC2011, was held in Incheon, Korea (Jan. 11-14, 2011). Euna Jeong has presented the research paper "Ontology-based instance data validation for high-quality curated biological pathways, by Euna Jeong*, Masao Nagasaki*, Kazuko Ueno, and Satoru Miyano (*equal contributor)," which will be published in BMC Bioinformatics on February 15, 2011.

The oral presentation is available at the Biological Research Information Center (BRIC).

MIRACH 1.0 paper published - January 2011

bioinformatics

The paper "MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models." by Hock Koh C, Nagasaki M, Saito A, Li C, Wong L, Miyano S is published by Oxford Journals' Bioinforamtics in the Bioinformatics Advance Access on January 5, 2011. MIRACH is our efficient Model checker for verifying specified properties of biological pathway models. You can find the abstract and full text here...

Cell Illustrator book (Korean version) has been published on Nov. 20, 2010

cibook-kr

Happy New Year!

The Korean version of our book "What does Systems Biology do? - Let's start with Cell Illustrator-" translated by Jin Hwan Do and Euna Jeong has been published on November 20, 2010.

Click here to see the Product Details of the book in Korean.

Contributions to the new book

book2010

Ayumu Saito, Masao Nagasaki from Miyano lab and Prof. Matsuno from Yamaguchi University, have contributed to write the chapter of the new book "Modeling in Systems Biology". The book will be published on October 22, 2010 by Springer.

They have written the part entitled "Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling" in Part II: Modeling Techniques.

The book can be accessed from this website and Amazon.

Prof. Chaouiya visited Miyano Lab

Chaouiya-san

Prof. Claudine Chaouiya first visited Miyano Lab in Sep. 9, 2010. We discussed about the application of Petri net to the field of Systems biology. Prof. Chaouiya gave the presentation about her group's recent research, for example, the analysis by using logical model, model checking and so on.

Prof. Chaouiya and Chen Li are the members of Program Committee of the Workshop on Biological Processes and Petri Nets (BioPPN2011). BioPPN2011 is the satellite workshop of PETRI NET 2011 and ASCD 2011, which will be held in June 20-24, 2010, Kanazawa, Japan. We encourage submissions of your inspired contributions relating to all aspects of the application and theory of Petri nets to Systems biology. Program of BioPPN2010 can be accessed from the website for your consideration.

Click HERE to visit Prof. Claudine Chaouiya's Homepage.

The official HP of PETRI NET 2011 and ASCD 2011.

Poster presentation in ISMB2010@Boston

ismb2010-poster

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 =>

Paper accepted for publication by BMC Systems Biology

bmc-astd

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 in Tokyo

bmc-modelchecking

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.

New Jounal Paper Published in In Silico Biology

bmc-modelchecking

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.

Mini-Genome Square 2009 in Fukuoka, Japan

minigsquare

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 in Akihabara, Japan

genomesquare09

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 in the 10th BioPathways Meeting in Stockholm (ISMB/ECCB 2009)

ISMB/ECCB2009

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.

New Jounal Paper Published in BMC Systems Biology

bmc-modelchecking

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.

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

cibook-en

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.

INBIOSIS Seminar 02

bmc-transpath

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 in Nagoya, Japan

bmc-transpath

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

Paper accepted for publication in BMC Systems Biology

bmc-transpath

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 in the Institute of Medical Science

h20ims

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.

News Announcement of CIO Release on SBML.org

CI_on_SBML

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 with CSML + BIOBASE TRANTHPATH

biobaseCIO

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.

Masao Nagasaki gave an oral presentaion at the conference of JSBi 2007

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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.

An article will appear in an issue of Journal of Wako Pure Chemical Industries, Ltd. (Infomatic World)

Journalofwako

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

Poster presentation in the 7th International Workshop on Advanced Genomics New Horizon

GenomeSquare07Poster

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 =>

Genome Square 2007 in Osaka

GenomeSquare07Poster

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.

Abstract in Japanese| Full poster image

Poster presentation in Life Science Research Network Symposium 2007

ISMB2007Poster

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.

Full poster image | Distribution version

Poster presentation in ISMB/ECCB 2007

ISMB2007Poster

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).

Link to the website for the long abstract =>

Show poster image =>

CI Book (Japanese) has been published in July, 2007

CI 3.0 Image

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.

See details here =>

Cell Illustrator 3.0 are released

CI 3.0 Image

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.

Poster presentation in PSB2007

PSB2007Poster

In early January, We announced the CSML world in PSB2007--Pacific symposium on biocomputing. The poster is now available. >> show image

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.

CSML 1.9 parser released.

CSML version 1.9 xml schema released.

draft version of CSML 3.0 released.

CSML version 1.9 specification released.

CSML version 1.0 xml specification and schema released.