Environment for an integrative model simulation: PLATO
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1
RIKEN, Computational science research program, Japan
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2
RIKEN Brain Science Institute, Japan
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3
Aichi Prefectural University, Japan
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4
The University of Electro-Communications, Japan
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5
Chubu University, Japan
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6
Chukyo University, Japan
The brain presides essential roles of human life, and fulfills precise and flexible processing generated by its complicated network. To elucidate the signal processing carried out by our nervous system, numerous physiological experiments and computational studies have been conducted. Those researches have revealed a great deal of brain function; however, a wealth of resources obtained in those experiments and modeling studies were mainly used for publishing articles. Currently, several neuroscience databases (e.g. platforms in INCF Japan-node, modelDB) started managing such resources (experimental data, articles, analysis tools, models) for preserving and sharing. To further elucidate the brain function systematically, the resources available on those databases should be integrated into a large-scale model where anatomical and physiological characteristics are explicitly implemented.
For this purpose, we have been developing a modeling environment called PLATO (Platform for a coLlaborative brAin sysTem mOdeling) which allows computational models to be constructed using several programming languages and connected by means of the common data format (e.g. netCDF, HDF5). It also provides a data management system and programming libraries to systematically build a large scale system model. In the present study, we introduce the PLATO and its newly developed programming libraries, which manage the data exchange and simulation of the large-scale model developed on the PLATO.
The PLATO consists of data management tool (Concierge), the common data format and its programming libraries, and simulation cluster server. The data management tool is utilized for searching and managing the resources to develop models. On the PLATO, the model integration is implemented in the common data format and its programming libraries at the I/O level. The programming libraries for the common data format support development of individual models as well as model integration. The common data format can include both data and its metadata; e.g. modeling convention, which describes the I/O configuration between models such as data name, its dimension and unit, and interval of data storing. Therefore, the common data format itself provides all the necessary information about the data as well as model I/O. It is also independent on operating systems and programming languages, and models can be made pluggable by applying the common data format. This property will be essential to integrate models developed by different programming environment, and be helpful to execute the integrated model on a parallel-processor computer system, especially on cloud computers. When the I/Os in the integrated models complies with the common data format and its programming libraries, an agent system in the library manages the execution of models and data exchange between models during simulation, where the simulation step, data I/O, and its timing are automatically adjusted considering MPI communication in each model.
The PLATO tightly collaborates with the neuroinformatics platforms available on the INCF Japan-node, because numerous models and physiological data are continuously registered on them. That is, the PLATO can provide multidisciplinary modeling environment by this collaboration. Finally, we hope that the PLATO will help researchers to develop models and to integrate them for constructing a large scale brain model in near future.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Poster Presentation
Topic:
General neuroinformatics
Citation:
Inagaki
K,
Kannon
T,
Kamiyama
Y,
Satoh
S,
Kamiji
N,
Hirata
Y,
Ishihara
A,
Shouno
H and
Usui
S
(2010). Environment for an integrative model simulation: PLATO.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00048
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Received:
11 Jun 2010;
Published Online:
11 Jun 2010.
*
Correspondence:
Keiichiro Inagaki, RIKEN, Computational science research program, Wako, Japan, kay@isc.chubu.ac.jp