• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Visual model checking approach of high level Petri-net and its application to dynamic biological pathway model

Research Project

Project/Area Number 20700265
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

NAGASAKI Masao  The University of Tokyo, 医科学研究所, 助教 (90396862)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2009: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2008: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsペトリネット / オントロジー / 視覚的デバッグ / モデル検査 / OWL / HFPNe / 細胞分化 / ASTD
Research Abstract

The pathway modeling and simulation architecture named (Hybrid Functional Petri net: HFPNe) has been developed and implemented. In this research, a model checking concept is introduced to the HFPNe. A simulation model of C. elegans cell fate determination is created using HFPNe and the reasonable rule of the cell fate determination is selected by using the model checking approach. Furthermore, an algorithm to extract the active sub-pathways from a given HFPNe model and the trajectory of these sub-pathways is developed. The applicability is demonstrated using the circadian clock simulation model with HFPNe.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (13 results)

All 2010 2009 2008 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results) Remarks (2 results)

  • [Journal Article] Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram2010

    • Author(s)
      Li C*, Nagasaki M*, Saito A, Miyano S.
    • Journal Title

      BMC Systems Biology 4

      Pages: 39-39

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Time-dependent structural transformation analysis to high-level Petrinet model with active state transition diagram2010

    • Author(s)
      Li C, Nagasaki M, Saito A, Miyano S.(Equal contributor)
    • Journal Title

      BMC Systems Biology 4:39(online journal)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A computational platform for systems biology2009

    • Author(s)
      Nagasaki, M., Saito A., Jeong E, Li C., Kojima, K, Ikeda, E., Miyano, S
    • Journal Title

      Cell Illustrator 4. 0 10

      Pages: 2-2

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension2009

    • Author(s)
      Li, C. *, Nagasaki, M. *, Ueno, K., Miyano, S.
    • Journal Title

      BMC Systems Biology 3

      Pages: 42-42

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cell Illustrator 4.0 : A computational platform for systems biology. 10:00022009

    • Author(s)
      Nagasaki, M., Saito A., Jeong E, Li C., Kojima, K, Ikeda, E., Miyano, S.
    • Journal Title

      In Silico Biology 10:0002(online journal)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simulation-based model checking approach to cell fate pecification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension2009

    • Author(s)
      Li, C., Nagasaki, M., Ueno, K., Miyano, S.(Equal contributor)
    • Journal Title

      BMC Systems Biology 3:42(Online journal)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid function Petri net with2009

    • Author(s)
      Chen Li^*, Nagasaki M^*, Ueno K, Miyano S (equal contributor)
    • Journal Title

      BMC Systems Biology 3:42(online journal)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong E, Nagasaki M, Miyano S.
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

    • Author(s)
      Nagasaki M, Saito A, Li C, Jeong E, Miyano S.
    • Journal Title

      BMC Systems Biology 2

      Pages: 53-53

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Rule-based reasoning for system dynamics in cell systems2008

    • Author(s)
      Jeong E, Nagasaki M, Miyano S
    • Journal Title

      Genome Informatics 20

      Pages: 25-36

    • NAID

      130003997509

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Systematic reconstruction of TRANSPATH data into Cell System Markup Language2008

    • Author(s)
      Nagasaki M, Saito A, Li C, Jeong
    • Journal Title

      BMC Systems Biology 2

      Pages: 53-53

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Remarks]

    • URL

      http://www.csml.org/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.csml.org/

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2008-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi