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Databases for multilevel biophysiology research available at Physiome.jp.

Yoshiyuki Asai1, Takeshi Abe1, Li Li2

  • 1Integrated Open Systems Unit, Okinawa Institute of Science and Technology Graduate University Okinawa, Japan.

Frontiers in Physiology
|October 7, 2015
PubMed
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Physiome.jp offers updated tools and databases for physiome and systems biology research. Enhancements support collaborative model development and simulations within an integrated framework.

Area of Science:

  • Physiome and Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Physiome.jp was established in 2007 to facilitate model-based research.
  • The portal provides tools and databases for constructing physiological, multi-hierarchical, and large-scale models.
  • It houses databases for mathematical models, morphological data, and time-series data.

Purpose of the Study:

  • To describe the updates and new functions implemented in Physiome.jp since 2013.
  • To highlight the enhanced information infrastructure supporting collaborative model development and simulations.
  • To detail improvements in database cooperation, model browsing, user and version management, parameter sets, and application interoperability.

Main Methods:

  • Database renovation and implementation of new functions in 2013 and 2015.
Keywords:
databasesinteroperability among databasesinteroperability with applicationsmodel sharingmultilevel modelsphysiome and systems biologyteam development

Related Experiment Videos

  • Integration of three distinct databases (mathematical models, morphological data, time-series data).
  • Development of features for interactive model browsing, user management, model versioning, parameter set management, and application interoperability.

    • Main Results:

    • The updated Physiome.jp provides a robust information infrastructure for physiome and systems biology.
    • Enhanced cooperation among databases facilitates integrated research.
    • New functionalities enable collaborative model development, simulation, and data management.

    Conclusions:

    • Physiome.jp has evolved into a comprehensive platform supporting advanced model-based research.
    • The implemented updates significantly enhance collaborative research capabilities in physiome and systems biology.
    • The portal serves as a vital resource for the scientific community engaged in developing and utilizing physiological models.