Integrating the BioExtract Server with the iPlant Collaborative

University Of South Dakota Main Campus, Vermillion SD

Investigators

Abstract

PI: Carol Lushbough (University of South Dakota) Collaborators: Stephen Goff (University of Arizona), Daniel Stanzione (University of Texas - Austin), Volker Brendel (Iowa State University) and Molly Nepokroeff (University of South Dakota) The BioExtract Server is an open, Web-based system designed to aid researchers in the analysis of genomic data by providing a platform to facilitate the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and Web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. The iPlant Collaborative (www.iplantcollaborative.org) is a project sponsored by the National Science Foundation to build a computer infrastructure for research in the plant sciences. By sponsoring distributed informatics projects, iPlant extends high level computation to researchers through access to data, analytic tools, and workflows. One of the primary goals of the iPlant Collaborative is the reuse and integration of relevant technology that exists in the science community and to collaborate with other researchers when building new infrastructure. The overall goal of this project is to make data, analytic tools, and workflows accessible, interoperable, easy to use, and applicable to research and education. In collaboration with the iPlant Collaborative, this project will enable researchers to execute iPlant analytic tools within the BioExtract Server, create iPlant workflows through the BioExtract Server, and manage analysis and provenance data across both platforms. Examples of such management include executing BioExtract Server tools and workflows and creating data extracts with input drawn from iPlant, storing BioExtract Sever tool results at iPlant, and annotating iPlant data through the BioExtract Server. The primary, overall objective of this project is to make data, analytic tools, and workflows accessible, interoperable, easy to use, and applicable to research and education. As the project's functionality becomes available through the BioExtract Server (bioextract.org) / iPlant (www.iplantcollaborative.org) platforms, it will be introduced to the research and educational communities through workshops, presentations, publications, and education. BioExtract Server integrated functionality will be added to the content of iPlant's free, 2-day "iPlant Genomic Education Workshops" which instruct researchers and faculty in the use of iPlant resources. The iPlant Collaborative holds more than 10 on-campus training sessions per year, in addition to workshops at a number of major conferences (including the ASPB Annual Meeting and the Plant & Animal Genome Meeting for the plant community, and the SC conference series for the computing community). Through these workshops, project personnel will demonstrate how the integrated iPlant/BioExtract Server functionality can be applied to general research questions. Personnel will work with individual researchers to help identify ways in which the integrated functionality could be leveraged to perform specific analysis. In addition to creating and delivering workshop content, the project will create videos demonstrating the iPlant/BioExtract Server functionality. These videos will be made available through the iPlant website as well as the BioExtract Server site. Finally, project functionality will be incorporated into yearly BioExtract Server workshops for the Undergraduate Research Fellows from the partner institutions of South Dakota NIH NCRR's IDeA Networks of Biomedical Research Excellence (INBRE) for which the PI serves as the Bioinformatics Core Director. Finally, the BioExtract Server will be an independent system available through an open source license that can be installed on individual servers. Individual installations will be configurable and allow for the inclusion of resources that best fit individual project needs.