BioSupercomputing Newsletter Vol.4

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Report on Research
Brain and Neural WG
PLATO: Platform for a collaborative brain system modeling toward development of large scale mathematical model.

1) Computational Science Research Program, RIKEN
2) Brain Science Institute, RIKEN
Keiichiro Inagaki 1) Takayuki Kannon 2) Nilton L. Kamiji 2) Koji Makimura 2)
Shiro Usui 1) 2)

Keiichiro Inagaki, Takayuki Kannon, Nilton L. Kamiji, Koji Makimura, Shiro Usui

The elucidation of information processing fulfilled by the brain is regarded as the most difficult problem in natural science. In the brain, about 100 billion nerve cells form a network consisting of about 1 trillion contacts known as synapses. It is thought that various information obtained from the external world, such as vision and audition, is processed flexibly and appropriately by this network in the brain. The function of such complicated information processing in the brain is being revealed mainly by electrophysiological experiments. Together with the recent dramatic progress made in computational science, research to elucidate brain functions from the perspective of computational science has also been conducted by structuring part of the brain in detail as a mathematical model, and carrying out simulations. However, it is still difficult to describe the whole brain as a large-scale mathematical model for simulation.

Since a vast amount of knowledge and sophisticated techniques are required to construct a large-scale brain model, it is difficult for a researcher to achieve this by working alone. Therefore, it is considered rather impor tant to collec t and accumulate the knowledge obtained by the collaborative work of various researchers, and to integrate it as a large-scale model running on a computer. We are now designing a method to integrate the knowledge and mathematical models concerning various sites of the brain obtained from conventional physiological and computational research as a novel approach for constructing a large-scale brain model. In our approach, we are constructing an integrated development environment consisting of tools for collecting and managing the data required for development and simulation of models registered in the database server such as ModelDB at Yale University and various platforms of Neuroinformatics Japan-Node, simulators, simulation server, and a result visualization tool (Figure 1). In order to facilitate interconnection of multiple models, we are studying and developing a data format to standardize the input and output of the model for data exchange, and its supporting library. The common format, for example, would make it possible to connect mathematical models produced with different programming languages and/or simulator s, such as C language and Python. Since the model input and output are standardized, we can modify and update a model into a large-scale model and install a new mathematical model in a plug-in manner. Interconnected models are simulated in parallel by a system called Agent. During the simulation, data communication between models is also adjusted automatically by accounting the progress of each model. By providing a unified library for such a common format and Agent, it is expected that the creator of the model can develop a mathematical model that can bind to other models without changing most of the program codes.

For describing the information processing underlying "vision", one of the brain functions, we are constructing a large-scale model of the whole visual system by the approach we have described. The human visual system consists of eyes, optic system, retina and cerebral cortex, where information from the external world are processed at these multihierarchicall sites to achieve functions such as recognition of objects and transition of visual lines. By constructing mathematical models for various sites in the brain, integrating them by the method we described and doing simulations, we hope to visualize the information processing that occurs when humans look at an object, for example visual illusion such as in Figure 2. In the future, by describing all the sites in the brain involved in “vision” in collaboration w ith v ar ious res earch er s invo lve d in this f iel d, integrating them by the approach that we proposed, and performing computer simulation as a large-scale model of "vision" using K computer, it will become possible to elucidate the visual information processing that occurs in the brain.

Figure 1 : PLATO system
Figure 1 : PLATO system environment PLATO consists of 4 environments including a data management tool (http://, model development environment, simulation server and the result drawing tool.

Figure 2
Figure 2. Configuration diagram of a large-scale visual system model S c h e m a t i c d i a g r a m o f a n integrated mathematical model of the visual system comprising of the eye movement, the optic system, the retina and the cortex, a n d s a m p l e i m a g e o f e a c h model output at simulation. The mathematical model at each site is described as an individual model, and each model is connected by the common format (Common data format).

BioSupercomputing Newsletter Vol.4

In order to change from observation-type medical practice focusing on experience to prediction-type medical practice to construct the base of theoretical medicine
Professor, Department of Internal Medicine (Cardiovascular Medicine), Director of the Metabolic Disease Research Center, Bio-Research Medical Center, Tokai University Graduate School of Medicine, and Director, Department of Metabolic System Medicine, Tokai University General Medical Laboratory Shinya Goto
It is expected that new possibilities in nutrition science and health control will be opened up
by simulation science

EXECUTIVE PROFESSIONAL Health infomatics DEPT., Ajinomoto Co., Inc. Toshihiko Ando
Report on Research
The functions of a multidrug discharging transporter were verified by coarse graining molecular simulation (Molecular Scale WG)
Graduate School of Science, Kyoto University Shoji Takada / Xin-Qiu Yao / Hiroo Kenzaki
Cell simulation considering time-space (Cell Scale WG)
Computational Science Research Program, RIKEN Yasuhiro Sunaga
Development of HIFU simulator for non-invasive treatment with high-intensity focused ultrasound (Organ and Body Scale WG)
VCAD System Research Program, RIKEN Kohei Okita
PLATO: Platform for a collaborative brain system modeling toward development of large scale mathematical model.(Brain and Neural WG)
①Computational Science Research Program, RIKEN
②Brain Science Institute, RIKEN
Keiichiro Inagaki①/ Takayuki Kannon②/ Nilton L. Kamiji②/ Koji Makimura②/ Shiro Usui ①②
Report on the workshop in BMB2011 (Joint Meeting of the 33rd Congress of the Molecular Biology Society of Japan and the 83th Congress of the Japanese Biochemical Society)
Winter School 2011 for the Integrated Simulation of Living Matter
Computational Science Research Program, RIKEN Yasuhiro Ishimine (Organ and Body Scale WG)
The Institute of Medical Science, The University of Tokyo Hidetoshi Urakubo (Brain and Neural WG)
Computational Science Research Program, RIKEN Yasuhiro Sunaga (Cell Scale WG)
Computational Science Research Program, RIKEN Gen Masumoto (High-Performance Computing Team)
Computational Science Research Program, RIKEN Keiji Misawa (Data Analysis Fusion WG)
Computational Science Research Program, RIKEN Hisayuki Miyashita (Molecular Scale WG)
ISLiM Participating Institutions / Event Infomation / Event report