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Welcome to PathCase Family of Applications

Each PathCase application below contains a different set of tools. All applications store, query, and visualize metabolic pathways, in addition to their specialized tasks. For more information on each PathCase application, please check out the links located below.

Current Research

This system, currently being developed by a grant from NSF Biology, integrates metabolic pathways with systems biology models. The aim of the PathCaseSB project is to build a framework and tools towards effective and efficient systems biology model development for multiscale mechanistic models of biological systems.

Data Sources Used: BioModels models and KEGG pathways

Click here for more info ...

Current Research

This site is a clone of PathCaseSB site mentioned above and instead of hosting BioModels models, it hosts SBML Test Suite models.

This system, currently being developed by a grant from NSF Biology, features mammalian metabolic pathways and computational tools designed for metabolomics analysis. Towards this end, PathCaseMAW database contains a fully hierarchically compartmentalized metabolic network for mammalian (humans and mice).

Data Sources Used: Mamalian pathways from literature.

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This system features KEGG metabolic pathways. That is, it contains in its database, KEGG metabolic pathways. KEGG pathways data in PathCaseKEGG database is refreshed annually every year, via a license from KEGG.

Data Sources Used: KEGG Pathways

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This system is the gateway to sister PathCaseMAW sites of three reconstructed metabolic networks.The data is from different sources of literature for different organisms and different models.

This system features sample pathways from the literature, and is no longer updated.

Data Sources Used: Literature

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This system features BioCyc human pathways. That is, it contains in its database, BioCyc human pathways. It is no longer updated in that we do not refresh its database with recent changes in BioCyc human pathways.

Data Sources Used: BioCyc human pathways

Click here for more info ...

What is New?

>> August 2011
  • Ercument Cicek, Xinjian Qi, En Cheng, Lei Yang presented three papers in ACM-BCB 2011 in Chicago.
  • Model Composition Tool is released and short video is available on Youtube.
>> July 2011
  • Under Xinjian Qi's supervision Steve Johnson developed an Apple iPad application for MAW project. You can download the application from Apple iTunes for free.
>> April 2011
  • Prof. Nicola Lai has received a grant from the National Institute Of Arthritis And Musculoskeletal And Skin Diseases (NIH/NIASM) for "Systems Biology Investigation of Muscle Exercise Metabolism in Diabetes" project.
>> February 2011
  • Example models(with Matlab code, SBML model, and model description) by Prof. Nicola Lai are added to compare model simulators section of the web site.
>> August 2010
  • Version 4.0 of PathCaseSB is released. The main functional components are PathCaseSB Browser Interface, PathCaseSB Querying Interface, PathCaseSB Simulation Interface, and the PathCaseSB Provenance Tool.
  • Version 1.0 of PathCaseMAW is released. The main functional components are Observed Metabolite Analysis (OMA) tool, and reworked versions of PathCaseMAW Browser Interface, PathCaseMAW Querying Interface and the new PathCaseMAW database with fully hierarchically-arranged compartments.
  • The poster titled Efficient Query Evaluation for DAG-Shaped Hierarchies written by En Cheng, Ali Cakmak, Z. Meral Ozsoyoglu is presented in ACM-BCB2010.
  • The full-paper titled Analyzing Metabolomics Data for Automated Prediction of Underlying Biological Mechanisms written by Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Ozsoyoglu is presented in ACM-BCB2010.
>> June 2010
  • Sarp Coskun and Ercument Cicek presented two posters titled PathCaseSB: Database-Enabled Tools for Regulatory Metabolic Networks, PathCaseMAW: Pathcase Metabolics Analysis Workbench in OCCBIO.
Click here to see events before June 2010.

See the countries and domains of PathCase users during (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 .