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July 17, 2013
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July 22-25, 2013
The 2013 World Congress in Computer Science, Computer Engineering, and Applied Computing

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WORLDCOMP'13 Tutorial: Drs. Carol Lushbough & Rion Dooley

Last modified 2013-07-07 17:54

Creating Bioinformatic Workflows within the BioExtract Server Leveraging iPlant Resources
Dr. Carol Lushbough 1 & Dr. Rion Dooley 2

1 Department of Computer Science, University of South Dakota, USA
PI, National Science Foundation, Integrating the BioExtract Server with the iPlant Collaborative

2 Texas Advanced Computing Center, University of Texas at Austin, USA

Date: July 24, 2013
Time: 6:00pm
Location: Montecristo 4


    In order to handle the vast quantities of biological data generated by high-throughput experimental technologies, the BioExtract Server ( has leveraged iPlant Collaborative ( functionality to help address big data storage and analysis issues in the bioinformatics field. The BioExtract Server, a National Science Foundation (NSF) sponsored project, is a Web-based, workflow-enabling system that offers researchers a flexible environment for analyzing genomic data. It provides researchers with the ability to save a series of BioExtract Server tasks (e.g. query a data source, save a data extract, and execute an analytic tool) as a workflow and the opportunity for researchers to share their data extracts, analytic tools and workflows with collaborators. The iPlant Collaborative, funded by NSF, is a community of researchers, educators, and students working to enrich science through the development of cyberinfrastructure - the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services– that are essential components of modern biology. The iPlant Foundation API, developed through the iPlant Collaborative, is a hosted, Software-as-a-Service resource providing access to a collection of High Performance Computing (HPC) and Cloud resources. Leveraging the iPlant Foundation API, the BioExtract Server gives researchers easy access to multiple high performance computers and delivers computation and storage as dynamically allocated resources via the Internet.

    We will introduce researchers to the iPlant Foundation API and show how it was integrated into the BioExtract Server making iPlant resources easily available. Researchers will be introduced to the BioExtract Server functionality of querying data sources, saving data extracts, executing iPlant and other analytic tools, using data from the iPlant Discovery Environment (DE) as input into an analytic tool, storing output from analytic tools to the iPlant DE, creating and executing bioinformatic workflows, and sharing workflows with others.


    The primary objectives of this tutorial are to acquaint researchers with the BioExtract Server functionality and how the system leverages the iPlant Foundation API. It is designed to demonstrate how researchers are able to easily access distributed analytic tools and data, including those in the iPlant Environment, in the creation of bioinformatic workflows.

Intended Audience

    The target audience includes scientists from different fields including Biologists and Software Developers, from various levels including researchers, educators, graduate students, and other scientific staff who either work with biological global data or are interested in understanding how to incorporate such data into their specific research workflows.

Biography of Instructors

    Carol Lushbough is an Assistant Professor of Computer Science at the University of South Dakota. She is the Principle Investigator on the National Science Foundation Project, IOS-1126481 Integrating the BioExtract Server with the iPlant Collaborative.

    Rion Dooley is a Research Associate and the Manager of the Web & Cloud Services Group at the Texas Advanced Computing Center, University of Texas at Austin.

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