What is New:

• For several additional KEGG pathways, curated layouts have been made available. To access the list of pathways with curated layouts, please go to built-in queries, then select "Visualize a set of pathways" query. The box at the top provides the list of pathways with curated layouts. This feature is presently available only for KEGG and sample pathways databases, and will be made available soon for the other databases as well.
• PathCase now has a site-wise keyword search facility.
• A "Quick Search" box added at the top, which enables users to pose keyword searches from any page that they browse at the time.
• Pathways are now visualized in boxes which highlight pathway borders. Each box also contains the pathway name. Shared metabolites connecting pathways are carefully placed in between pathway boxes. This feature is useful especially when multiple pathways are visualized.
• KEGG data has been updated with the most recent public release as of July 2008.

• A new version of PathCase running on Biocyc Human pathways has been released (still in alpha version).
• For several KEGG pathways, curated layouts have been tailored and made publicly available.
• The visualization applet now allows users with administrative privileges to modify and save layouts for pathways.
• Cofactors are now drawn as curved edges which makes it easier to distinguish cofactors from other reactants.
• Visualization of activators, inhibitors, and regulators are improved via careful positioning with respect to their reactions.
• PathCase has a new logo.

• The Advanced Query Interface now supports path and neighborhood queries and now has more descriptive text.
• Graph layouts are now improved and various minor improvements to the interactive visualizations.
• A tool, called BiopaxViz, has been integrated to allow users to visualize pathways in Biopax format.

• In the Advanced Query Interface, only values that can return results are presented as input suggestions.
• Built-in queries now allow for the user to specify a set of pathways on which they are executed.
• KEGG data has been updated with the most recent public release as of September 2007.
• Now supports Google Search within PathCase and a link to bookmark the current page.

• A built-in query is developed to search for pathways that are significantly enriched by a user-provided set of genes.
• PathCase now allows users to visualize any arbitrary select set of pathways through a built-in query.

• Advanced Query Interface (AQI) is released. AQI allows users to dynamically construct query interfaces that best fit to what they have in mind as a query.
• KEGG data has been updated with the most recent public release as of May 2007.

• A new PathCase version running on KEGG pathways data is released.
• Visualization now has a magnifier tool to instantly zoom into different parts of graphs
• Enzyme-only and Metabolite-only visualizations of pathways are integrated to PathCase.

• New graph layout algorithms are made available to the users with various user-adjustable parameters.
• A graph object explorer is developed to allow users to eliminate selected nodes.

• A new graph layout generation library (yFiles) has replaced previously used Tom Sawyer software which allows faster and scalable graph visualizations.
• Data model of the underlying PathCase database is made publicly available.

See the countries and domains of PathCase users in (2009), (2008), (2007), (2006), and (2005) since the release of the first version in August 2005.

Note: You must have version 1.6 or later of the Java browser plug-in installed on your system to view pathway graphs. To download the latest version of the free plug-in, go to Sun's JRE 1.6 (also known as version 6.0) download page.

This website is compatible with the latest versions of Firefox and Internet Explorer browsers. For questions or comments, please e-mail pathcase [at] case [dot] edu .