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Please join us for the new NRP Engagement meeting series for a presentation by Alex Feltus on
“Running Genomics Workflows on the Pacific Research Platform’s Nautilus Kubernetes Cluster”
(abstract below)
Monday, October 28, 2019 at 1 ET - 12 CT - 11 MT - 10 PT
Zoom: https://internet2.zoom.us/j/735965245
Feel free to share this announcement with anyone that may be interested. Calls will be on the fourth Monday of the month. To hear about future activities, please join the NRP engagement email list via this link.
Running Genomics Workflows on the Pacific Research Platform’s Nautilus Kubernetes Cluster
Alex Feltus, Ph.D.
Professor|Genetics & Biochemistry @ Clemson University; Co-Founder|Praxis AI
Our core biological research mission is to discover causal alleles underlying complex trait expression in plants and animals. Active projects include (A) discovery of genetic subsystems driving legume-microbe symbiosis that can be engineered into other plants so they can make their own fertilizer, (B) elucidation of gene expression pattern shifts between normal and disordered brain tissue for better diagnosis of intellectual disability, and (C) detection of tumor specific alterations in kidney and other tumors of relevance to precision medicine. Our scientific instrument is the high performance/throughput computer where we run bioinformatic, machine learning, and network biology workflows on tens to thousands of terabytes of in-house and open source deep DNA sequencing datasets. In recent years, we have wrapped applications in containerized NextFlow workflows and now run data intensive experiments on Kubernetes (K8s) clusters including the PRP Nautilus cluster (we have added a node at Clemson) and the Google Cloud Platform. In this webinar we will (A) present results from a large tumor biomarker screen generated with the Nautilus cluster, (B) describe broadly useful open source genomics workflows (GEMmaker, KINC, and Gene Oracle) with Nautilus-specific usage documentation, (C) outline a grassroots strategy to add nodes to the Nautilus cluster and train people how to use that super-awesome system, and (D) discuss a business model where one can build an elastic K8s cluster for a small virtual organization that can be dynamically linked to larger national compute fabrics platforms via aggregation or federation.
Dr. F. Alex Feltus received a B.Sc. in Biochemistry from Auburn University in 1992, served two years in the Peace Corps, and then completed advanced training in biomedical sciences at Vanderbilt and Emory. Since 2002, he has performed research in bioinformatics, high-performance computing, cyberinfrastructure, network biology, genome assembly, systems genetics, paleogenomics, and bioenergy feedstock genetics. Currently, Feltus is an Professor in Clemson University's Dept. of Genetics & Biochemistry, CEO of Allele Systems LLC, Core Faculty in the CU-MUSC Biomedical Data Science and Informatics (BDSI) program, member of the Center for Human Genetics, and serves on the Internet2 Board of Trustees as well as various "Advance Research Computing" engagement workgroups. Feltus has published numerous scientific articles in peer-reviewed journals, teaches undergrad and PhD students in bioinformatics, biochemistry, and genetics. At present, he is funded by multiple NSF grants and is engaged in tethering together extremely smart people from diverse technical backgrounds in an effort to propel genomics research from the Excel-scale towards the Exascale.