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What's new for release 2.0?

Since the release of version 1.0 on July 2003, more tools and features are added in the current release. We redesigned the database to capture gene and organism information in an integrated manner. The new release offers more reliable operations, better performance and enhanced services.
  • The Genome Pathway Browser takes the organism information into account. Organism can be viewed in different levels. In the application, users can set the organism information from three components.
    1. Set organism from the Pathway Browser,
    2. Set organism from the queries in the main menu,
    3. Set organism from the Pathway Viewer.
  • In Pathway Browser, users can set organism information at different levels. The organism setting of the top-most tree node controls its descendant organism settings. The organism settings can stay the same or be changed from more general to less general going from ancestors to descendants in the hierarchy. (For example, when the top-most tree node, say Pathways, organism property is set to “unspecifiedE users can set its descendant nodes, say processes, to a specific organism, say mouse, to browse the processes in mouse that belong to the given general pathway).
  • Genome Viewer is added and gene information is updated. Our current database stores thousands of human and mouse genes and proteins with cross links to Locus Link and Swiss-Prot. Users can query gene paralogs and orthologs from the Pathway Browser. With the Genome Viewer, genes for a pathway or a process can be drawn on the corresponding chromosome. From the genes in the Genome Viewer, users can initiate queries such as highlighting the processes on the graph that the selected gene is involved in. Currently, only Folate and Homocysteine pathway has complete human and mouse gene data [KT03]. The remaining pathways data is from the Gene Atlas [MG98] where instead of specific organisms, organism groups, (e.g. animal, plants) are provided.
  • Pathway Explorer is a new tool for this release.
  • Signaling pathway data is available to the browser. Signaling Pathway Browser is ready to use. However, the functionalities for drawing a signaling pathway as well as queries are not yet available at current release.
  • Better performance. Improved database design helped significantly for a better overall performance. For example, by exploiting the improved database design, the response time for the query “get the connected pathwaysEin the data viewer is now less than 2 seconds as compared to an average of more than 10 seconds in the previous version.
  • Easy installation. Utilizing the .NET setup makes this release a no-touch deployment. With no-touch deployment, the applications can be downloaded, installed, and run directly on the users' machines without any alteration of the registry or shared system components.

  1. [KT03] KITAMI, T., Data for Folate and Homocysteine Pathways in Mouse and Human, Department of Genetics, CWRU, Unpublished Manuscript, 2003.
  2. [MG98] Michal, G., Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, Wiley-Spektrum, 1998, ISBN: 0471331309.