Biochemistry

Abstract

CS-16-3 - Tripal: an open-source, standards-based toolkit for construction of online biological databases

Monday, July 16
3:58 PM - 4:18 PM

With the availability of large-scale, high-throughput data, challenges exist for research communities who desire to create online data repositories.  The financial, physical and personnel resources needed to create, maintain and improve a commuinty database can be overhwelming in comparision to the ease at which data is increasingly obtained.  These online databases fill an important niche specific to their respective research community by combining data with tools, custom searches, and visualizations not provided by larger online repositories.   Tripal is a popular, open-source toolkit developed to assist with the construction of online biological data repositories.  It is well suited for creation of genomics, transcriptomics and breeding databases and uses community-developed standards to provides data pages, search tools, and a graphical interface for site-specific customizations.    In addition to its default features, Tripal provides an Application Programming Interface (API) to allow a site developer to create new customizations, or extensions, that are specific for an individual site.  Moreover, an active community site developers share code, experience and expertise. Therefore, custom extensions can be shared with others, and this exchange helps decrease costs, ensure cross-site compatibility, and ensures long-term sustainabilty of all Tripal sites.   Recently, the Tripal Gateway Project, funded by the US National Science Foundation (NSF) award #1443040, has added functionality to address challenges related to storage, transfer, and analysis of large data. Specifically, three new capabilities are provided: 1) mechanisms for exchange of data between sites, 2) best practices for optimizing data transfers, and 3) integration with the Galaxy Project (an interface for execution of complicated scientific workflows) for large data workflow analysis.  Thus Tripal offers new sites model-organism style functionality, and supports large-data needs, but requires fewer resources.


 

Co-Authors

Chun-Huai Cheng – Washington State University; Shawna Spoor – Washington State University; Ming Chen – University of Tennessee; Abdullah Almsaeed – University of Tennessee; Bradford Condon – University of Tennessee; Nick Mills – Clemson University; Nick Watts – Clemson University; Connor Wytko – Washington State University; Lacey-Anne Sanderson – University of Saskatchewan; Emily Grau – University of Connecticut; Nic Herndon – University of Connecticut; Brian Soto – Washington State University; Sook Jung – Washington State University; Alex Feltus – Clemson University; Margaret Staton – University of Tennessee; Jill Wegrzyn – University of Connecticut; Dorrie Main – Washington State University

Stephen P. Ficklin

Assistant Professor
Washington State University

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CS-16-3 - Tripal: an open-source, standards-based toolkit for construction of online biological databases



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