Sponsor :

Global COE program “an in silico Medicine-oriented Worldwide Open Platform”

Co-Sponsor :

The Center for Advanced Medical Engineering and Informatics, Osaka University
Systems Biology Institute
Okinawa Institute of Science and Technology (OIST)


Okinawa Institute of Science and Technology (OIST)

7542,Onna,Onna-Son,Kunigami,Okinawa 904-0411, Japan

Tel : +81-98-966-8711
Fax : +81-98-966-8717


14 December 2009 - 18 December 2009


There are two main aims of the course. One is to disseminate the importance of the new integrative science so called physiome and systems biology to young researchers including doctoral course students in Asian-Pacific universities and institutes, who are studying in the fields of systems biology, chemical biology, computational biology, biological engineering, medical engineering, and bioinformatics. The other is to train them to be a leader of the fields in the next generation by contributing to promotion and development of these fields. Organizing this course in OIST as a host institute is completely consistent with the goal of OIST, which has a suitable environment to establish and develop new friendship among young participants.



Systems Biology and SBML, SBGN :

Systems biology is a biology-based inter-disciplinary study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Multiple scale modeling and simulations of human functions are necessary.
The Systems Biology Markup Language (SBML) is a XML-based computer-readable format for representing models of biochemical reaction networks in software. It's applicable to models of metabolism, cell-signaling, and many others. SBML has been evolving since mid-2000 thanks to an international community of software developers and users.
The Systems Biology Graphical Notation (SBGN) is an effort to standardize the graphical notation used in diagrams of biochemical and cellular processes studied in systems biology. Standardizing the diagrammatic notation is crucial for more efficient and accurate transmission of biological knowledge between different research communities in the expanding field of systems biology.
In this lecture overview of the systems biology and related technologies such as SBML and SBGN are summarized.

Physiome and insilicoML :

Physiome is a methodology to understand the integral of the human physiological functions in a similar manner of genome and proteome. The Physiome project aims at establishing databases of structure and functions of human physiology across multiple scales in time and space from molecular level to individuals, and integrate those data.
Since the physiological functions are represented as changes of states in time, building physiologically plausible mathematical models as dynamical systems of such physiological functions including morphology is an important methodology to carry on the physiome project. Since the Physiome project is targeting wide variety of subjects, sharing and reusing models is inevitable. The insilico Human project running in Osaka university has been developed a descriptive language of physiome-orienting models, called insilicoML (ISML) which is XML based language and can describe hierarchy and modularity of physiological functions in multiple levels.
In this lecture overview of the Physiome project going on in the world is summarized and insilicoML is explained.


CellDesigner :

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system, and are stored using the SBML which is a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner also performs simulations of models written in the SBML format.

insilicoIDE :

insilicoIDE is a model editor, simulator working with insilicoML. It provides graphical user interface to build up models. A module which is a principal unit constructing a model written in the insilicoML format, is represented as a ball and a relationship between modules is represented as a line called an edge. Equations and any other properties of a module are described in the module as its attributes. To run a simulation of a model, insilicoIDE convert it into C++ which supports MPI for parallel computation.


Time Table

Time Table (PDF)



Application form can be downloaded from here (Excel file) or here (PDF file). For Japanese, here (Excel file) or here (PDF file)


   16th October, 2009

   EXTENDED to 30th October, 2009

Every participant can apply for a financial award that will cover either your travel expense or registration fee, or both of them. Decision for the award grant will be made based on your application document and a recommendation letter submitted to the secretariat.


Access to OIST Seaside House (PDF)

Large Taxi (9 people can get on together) from Naha Airport to OIST Seaside House is arranged by the school.

Naha Ariport-->Naha City Center-->OIST Seaside House
1st taxi 14:20 14:40 15:50
2nd taxi 14:50 15:10 16:20
3rd taxi 16:10 16:30 17:40

If you do not take taxi, please take local public bus. Timetable is shown on this PDF file.


For further information or any questions, please contact:
Secretariat for Winter School on Computational Modeling in Biology
supported by:
The Systems Biology Institute
The Center for Advanced Medical Engineering and Informatics at Osaka University
E-mail: psb-ws __at__