Mark Miller

Principal Investigator, management, tool interface development, and customer service

San Diego Supercomputer Center 9500 Gilman Drive La Jolla, CA 92093-0505

Research Program:

My research effort is called Next Generation Tools for Biology. It is focused on creating enabling software tools and infrastructure for Biology and Biomedical Applications. This program takes advantage of the unique character of the San Diego Supercomputer Center by initiating projects that combine emerging techniques from computer science and biology research communities with best practices in software development. The goal is to create end-to-end solutions that link educators and scientists with high end data and computational resources without requiring them to know how to code. Our flagship project is the CIPRES Science Gateway, a resource that provides biologists with easy, open access to community sequence alignment and tree inference codes run on large compute clusters. We have made these resources available both through a browser interface and programmatically, through a RESTful API. CIPRES has supported scientists around the world in completing analyses that have appeared in more than 12,500 scholarly publications.


I received my BS in Biology from Eckerd College in 1976, and my PhD in Biochemistry under Claudia Kent from Purdue in 1984. I came to UCSD for a postdoctoral stint with Joe Kraut, followed by a brief visit to the private side at Monsanto/Kelco. Pre-SDSC, I sampled from many areas of research, including phospholipid and steroid metabolism, eukayotic cell biology, heme enzyme structure:function relationships, kinetics, and metabolic engineering. In 2000, I was inspired by the use of technology and robotics at the Joint Center for Structural Genomics, and came to SDSC to help with the launch of that venture. I have continued to work with goal of using the vast IT resources at SDSC in support of Biological/BioMedical research. My current goal is to make access to computational resources easy and flexible.

The CIPRES Team:

  • Wayne Pfeiffer Distinguished Scientist; HPC Expert
  • Mark Zhuang Senior Software Engineer

Alumni Team Members:

  • Tony Chen
  • Terri Schwartz
  • Paul Hoover
  • R. Hannes Niedner
  • Rami Rifiaeh
  • Ashton Taylor
  • Lucie Chan
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