BioExtract Server, a Web-based workflow enabling system, leveraging iPlant collaborative resources

In order to handle the vast quantities of biological data generated by high-throughput experimental technologies, the BioExtract Server (bioextract.org) has leveraged iPlant Collaborative (www.iplantcollaborative.org) functionality to help address big data storage and analysis issues in the bioinformatics field. The BioExtract Server 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 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 Agave API (Agave), 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 [6]. Leveraging Agave, the BioExtract Server gives researchers easy access to multiple high performance computers and delivers computation and storage as dynamically allocated resources via the Internet.