A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation

• ASAI Yoshiyuki

  Okinawa Institute of Science and Technology Graduate University

• ABE Takeshi

  Okinawa Institute of Science and Technology Graduate University

• OKA Hideki

  RIKEN Brain Science Institute, Neuroinformatics Japan Center

• OKITA Masao

  Graduate School of Information Science and Technology, Osaka University

• HAGIHARA Ken-ichi

  Graduate School of Information Science and Technology, Osaka University

• GHOSH Samik

  The Systems Biology Institute

• MATSUOKA Yukiko

  The Systems Biology Institute

• KURACHI Yoshihisa

  Graduate School of Medicine, Osaka University

• NOMURA Taishin

  Graduate School of Engineering Science, Osaka University

• KITANO Hiroaki

  Okinawa Institute of Science and Technology Graduate University The Systems Biology Institute

Abstract

Specialized languages used for describing computational models in the field of systems biology and physiology, such as Systems Biology Markup Language (SBML), CellML, and Physiological Hierarchy Markup Language (PHML), have been devised to enhance effective model reuse and sharing among researchers for developing large, multilevel models. Each language has its own specialty. By combining two of these languages, i. e. SBML for illustrating subcellular phenomena and PHML for expressing supracellular dynamics, a novel technology has been developed to describe models of multilevel biophysiological systems. For practical use of the aforementioned languages, consolidated software applications providing intuitive graphical user interfaces are necessary. Starting from 2011, a versatile platform called PhysioDesigner has been developed for multilevel modeling of physiological systems based on PHML. In this article, we focus on the newly developed distinguishing features of PhysioDesigner and PHML for the development of multilevel biophysiological models using SBML-PHML hybridization.

Journal

• Advanced Biomedical Engineering

  Advanced Biomedical Engineering 3 (0), 50-58, 2014

  Japanese Society for Medical and Biological Engineering

Keywords

• multilevel modeling
• SBML-PHML hybrid modeling
• PhysioDesigner.

Details

• CRID: 1390001205502981248
• NII Article ID: 130005001705
• DOI: 10.14326/abe.3.50
• ISSN: 21875219
• Web Site: https://www.jstage.jst.go.jp/article/abe/3/0/3_50/_pdf
• Text Lang: en
• Data Source:
  • JaLC
  • Crossref
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed