Biological Computing Using the iPlant Discovery Environment

Once the domain of large multi-institutional projects, genome-scale sequencing is now accessible to the individual researcher with the advent of low-cost ultra high-throughput methods. Lagging behind is the ability of individual researchers to handle and interpret the resulting large-scale data sets due to lack of access to computer resources, software, and technical training. The iPlant Collaborative is a U.S. National Science Foundation program to promote broad interdisciplinary collaboration and access to state-of-the-art information technologies through the provision of a cyberinfrastructure.  Here we describe tools and services available through iPlant’s Discovery Environment (DE).  The DE provides a web interface and platform to facilitate data handling and exploration by integrating analytical tools as modular components to be used individually or in workflows.  For researchers, the DE gives access to iPlant’s expansive data store and to over 300 open-source tools for genomics research.  Current tools encompass next-generation sequence analysis, assembly, transcriptome profiling, ChIP-seq, variant-detection, association studies, phylogenetic analysis and trait evolution, among others.  Computes are run on standard or high performance computing nodes depending on the throughput and resources needed.  For scientific developers, the DE provides a venue to expose new software and the potential to exploit high-performance computing provided by the Texas Advanced Computing Center’s XSEDE.  The DE will ultimately strengthen the scientific community by serving as a marketplace to share ideas and facilitate scalable collaborative research.  The iPlant Collaborative is funded by NSF #DBI-0735191.