iMicrobe: Advancing Clinical and Environmental Microbial Research using the iPlant Cyberinfrastructure

Microbes are fundamental drivers of ecosystem function both in the environment and in animal/human health.  Large-scale metagenomic sequencing efforts, such as the Human and Earth Microbiome projects have yielded new datasets that make it possible to explore these complex microbial communities and how they change across both space and time.  Yet, given the fast-paced development new strategies for analyzing metagenomic datasets and advances in big data science for computing, cutting-edge tools for microbial research remain in a subset of highly proficient labs.  To democratize access and development of community tools, in a scalable computing environment, we have begun developing a microbial-centric resource called iMicrobe that leverages the existing open-source iPlant cyberinfrastruture.  Specifically, we use iPlant for: (i) the scalable upload and controlled sharing of data and results by users, (ii) development of state-of-the-art microbial data processing pipelines and Apps, (iii) distribution of open source code, and (iv) compute resources provided by condor (grid computing) and XSEDE (distributed computing). Since the iMicrobe project was initiated in June 2013, 11 new Apps have been developed and two high-performance computing pipelines.  Lastly, given capabilities in iPlant to maintain and query metadata, we are exploring new ways to promote data discoverability and refined analyses in iPlant.  These resources allow us to promote the efficient sharing of data and compute resources, provide a platform for developers to securely build new algorithms and data processing pipelines for microbial ecology, and service the research community through interaction in a common ecosystem.