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About the Analysis Core

Our model is to work side-by-side with researchers to design and build analysis pipelines and cloud infrastructure as part of their larger projects. To that end, we work with researchers while writing grant proposals to ensure adequate computational resources are included for new projects. Following funding, we scale up our analysis on commercial or academic clouds to ensure projects receive their analyzed data as fast as possible.

Staff

Brian O’Connor

Technical Director of the Analysis Core

Dr. Brian O’Connor is the Technical Director of the UCSC Genomics Institute Analysis Core. He focuses on the development and deployment of large-scale, cloud-based systems for analyzing genomics data. This includes the Toil workflow execution platform, which is designed to run genomic pipelines on a wide range of cloud environments including AWS, Azure, Google and OpenStack, and ADAM, a distributed genomics platform developed in collaboration with UC Berkeley. He is also the co-chair of the Containers and Workflows task team of the Global Alliance for Genomics and Health (GA4GH) where he works on tool and workflow container standards. Brian recently joined UCSC from the Ontario Institute for Cancer Research (OICR) where his previous projects included leading the technical implementation of cloud-based analysis systems for the PanCancer Analysis of Whole Genomes (PCAWG) effort, the creation of the Dockstore project (http://dockstore.org), and the development of the International Cancer Genome Consortium’s Data Portal (http://dcc.icgc.org).

Walter Shands

Senior Software Engineer

Walt develops software for the Computational Genomics Platform (CGP) where his focus is on integration of bioinformatics pipelines such as RNA-Seq, ProTECT, and BCBio into the software infrastructure, running those pipelines on genomic data and developing new features. In addition he contributes to HMMER, a homology search application, most recently implementing translated search. Walt has a wealth of industry experience which includes significant contributions at Intel, Fujitsu and AT&T Bell Laboratories. Walt has both an M.S. and B.S from the School of Engineering at Columbia University in New York, and a black belt in Aikido.

Carlos Espinosa

Software Engineer

Carlos is a Software Engineer at the Computational Genomics Platform (CGP). He has been heavily involved in DevOps work, focused on integration and deployment using technologies such as Docker and docker-compose. He worked on the web service that powers the Platform's file browser and has been involved in prototyping a file viewer for HCA (Human Cell Atlas). His work uses Python, Flask/Chalice, and Elasticsearch. Carlos has a B.A. in Computer Science and a B.S. in Molecular, Cell, & Developmental Biology from UCSC.