Integration of cell designer and SABIO-RK

Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Hiroaki Kitano

Research output: Contribution to journalArticlepeer-review

47 Citations (Scopus)

Abstract

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge for systems biology. To facilitate this research topic, we have developed CellDesigner to visualize, model and simulate biochemical networks. CellDesigner allows the users to easily create networks using solidly defined and comprehensive graphical notation. CellDesigner utilizes SBML to described models and can simulate models using an integrated SBML ODE Solver or third party simulation engine; thus enabling users to simulate through a sophisticated graphical user interface. Although CellDesigner can integrate with existing databases (KEGG, PubMed, BioModels, etc.), by calling a web browser, or connecting to its web page through HTTP, integration with SABIO-RK has the potential to expand connectivity and semi-automate visualization and model building. SABIO-RK contains information about biochemical reactions, related kinetic equations and parameters. Also information about the experimental conditions under which these parameters were measured is stored. By using the Web service API provided by the SABIO-RK team, we have succeeded to directly connect to the database, send search queries by ID or name of its component, and then import the query results into CellDesigner.

Original languageEnglish
Pages (from-to)81-90
Number of pages10
JournalIn Silico Biology
Volume7
Issue numberSUPPL. 2
Publication statusPublished - 2007 Jun 11

Keywords

  • Biochemical simulation
  • Database integration
  • Kinetic modeling
  • SBGN
  • SBML
  • Systems biology
  • Web services

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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