Interoperability between multilevel modeling platform PhysioDesigner and databases in Physiome.jp and Dynamic Brain Platform through Garuda platform
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1
Okinawa Institute of Science and Technology, Japan
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2
E-Sir, Japan
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3
Intasect Communicatons Inc, Japan
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4
The Systems Biology Institute, Japan
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5
Kyushu Institute of Technology, Graduate School of Life Science and Systems Engineering,, Japan
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6
RIKEN, Neuroinformatics Japan Center,, Japan
In recent times, accumulation of considerable amounts of experimental data about various levels of physiological functions, from the level of protein to the body overall, accelerated growth of mathematical models in size and complexity. To develop detailed physiological models, a systematic supportive framework which can facilitate effective sharing and reuse of existing models is essential. It is important that such a supportive framework includes two components. One is model databases and the other is a system to assist modeling process.
The PhysioDesigner is a software platform available at http://physiodesigner.org that provides graphical support for the construction of mathematical models by explicitly expressing multiple hierarchies in physiological systems. In PhysioDesigner, structure and functions seen in physiology are managed as modules, and a model is constructed by defining relationships between the individual modules. Each module is quantitatively characterized by defining dynamics and constants. Models built on PhysioDesigner are written in Physiological Hierarchy Markup Language (PHML), a descriptive language designed to represent hierarchical structure and functional network of modules.
PhysioDesigner can interoperate with databases opened in the internet through database client applications supporting Garuda alliance (http://www.garuda-alliance.org), which mediates communication among applications. So far we have developed two client applications for databases in Physiome.jp and in Dynamic Brain Platform.
A portal site Physiome.jp was established in 2007 to release applications and databases supporting construction of physiological multilevel large-scale models. The portal is available at http://physiome.jp. In Physiome.jp, three kinds of databases are open to the public, which include a database of mathematical models written in PHML, and databases containing morphology and time series data.
Dynamic Brain Platform (DBPF) is one of neuroinformatics platforms promoted by the INCF Japan Node, in which there is a database including mathematical models of physiological functions, as well as other information, such as commentaries. It is accessible at https://dynamicbrain.neuroinf.jp.
To effectively utilize these data in the databases, client applications complying with Garuda alliance has been developed. The clients can seamlessly bridge information in the databases to tools, such as the modeling platform PhysioDesigner. The linkage can also be expanded to any other tools complying also with Garuda alliance. The seamless linkage between the databases and tools will greatly enhance usability of those data and promote development of models.
Acknowledgements
This work is partly supported by Neuroinformatics Japan Center (NIJC), RIKEN BSI.
Keywords:
multilevel modeling,
database,
application interoperability,
PhysioDesigner,
Physiome.jp,
Dynamic Brain Platform
Conference:
Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.
Presentation Type:
Poster, not to be considered for oral presentation
Topic:
Infrastructural and portal services
Citation:
Asai
Y,
Kuwae
K,
Li
L,
Kitano
H,
Wagatsuma
H and
Yamaguchi
Y
(2014). Interoperability between multilevel modeling platform PhysioDesigner and databases in Physiome.jp and Dynamic Brain Platform through Garuda platform.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2014.
doi: 10.3389/conf.fninf.2014.18.00019
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Received:
04 Apr 2014;
Published Online:
04 Jun 2014.
*
Correspondence:
Dr. Yoshiyuki Asai, Okinawa Institute of Science and Technology, Kunigami-gun, Okinawa, 904-0412, Japan, asai@yamaguchi-u.ac.jp