The CIPRES Science Gateway: A Public Resource for Phylogenetics
Dr Mark Miller, Principal Investigator, Biology, at the San Diego Supercomputer Center
The CIPRES Science Gateway is a public resource that enables browser and RESTful access to phylogenetics codes run on high performance compute resources available through the XSEDE program.
Over the past five years, CIPRES has run half a million jobs for 12,000 scientists around the world, and enabled more than 1,700 peer reviewed publications.
This talk will provide an overview of the evolution of the CIPRES Science Gateway: the challenges faced and lessons learned in launching new services in a production resource with a large user base.
The talk will also describe plans for implementing the CIPRES Notebook Environment, which will provide access to HPC resources via an interface based on the Jupyter notebook project. The Jupyter notebook represents an exciting new paradigm for interactive scientific computing, and incorporating it into CIPRES will enable many capabilities that are not readily available to many phylogenetics researchers.
Mark Miller received his BS in Biology from Eckerd College in 1976, and his PhD in Biochemistry from Purdue in 1984.
He came to UCSD (University of California, San Diego) for a postdoctoral position, and subsequently became research scientist at Monsanto/Kelco in San Diego. Through his work in these positions, he developed expertise in many areas of modern biology, publishing more than 40 papers in areas including phospholipid and steroid metabolism, eukaryotic cell biology, protein crystallography, heme enzyme structure: function relationships, electron transfer kinetics, and metabolic engineering.
In 2000 he joined the San Diego Supercomputer Center to explore the use of technology and robotics as part of the Joint Center for Structural Genomics. He founded the next generation tools for the Biology Group at SDSC in 2003, and has worked since then to develop informatics tools and software that support Biological/Biomedical research.
He is currently the lead of the CIPRES Science Gateway, a highly successful website that provides browser-based access to high performance computers for thousands of researchers.