Digital Library
Close Browse articles from a journal
<< previous    next >>
     Journal description
       All volumes of the corresponding journal
         All issues of the corresponding volume
           All articles of the corresponding issues
                                       Details for article 5 of 10 found articles
  Integration of CellDesigner and SABIO-RK
Title: Integration of CellDesigner and SABIO-RK
Author: Funahashi, Akira
Jouraku, Akiya
Matsuoka, Yukiko
Kitano, Hiroaki
Appeared in: In silico biology
Paging: Volume 7 (2007) nr. supplement-2 pages 81-90
Year: 2007-05-30
Contents: 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.
Publisher: IOS Press
Source file: Elektronische Wetenschappelijke Tijdschriften

                             Details for article 5 of 10 found articles
<< previous    next >>
 Koninklijke Bibliotheek - National Library of the Netherlands