iPlant Collaborator: BioExtract

The BioExtract Server (bioextract.org) is a workflow-enabling system that offers researchers a flexible environment for analyzing genomic data. The BioExtract Server provides: 1) a flexible querying and retrieval interface to National Center for Biotechnology Information (NCBI) and European Bioinformatics Institute (EBI) nucleotide and protein databases, 2) the ability to filter query results and use them as input into analytic tools, 3) a facility to save query results as data extracts which are integrated into the system as searchable data sets, 4) access to analytic tools including a large list of curated Web services, generic access to SOAP-based Web services and command line tools residing on the user’s local workstation, 5) 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 6) the opportunity for researchers to share their data extracts, analytic tools and workflows with collaborators. The iPlant Collaborative (www.iplantcollaborative.org) is a project sponsored by the National Science Foundation to build a Computer Infrastructure (CI) for research in the plant sciences to bring together people, computation, data, and instruments so that scientists can rapidly respond to the changing dynamics of discovery and innovation. iPlant functionality has been integrated into the BioExtract Server providing scientists with seamless access to data, analytic tools, and workflows. Through the BioExtract Server, scientists are able to execute iPlant analytic tools, use data residing in their iPlant Discovery Environment (DE) as input and store output to their DE.