Mark A. Miller
Mark A. Miller
Principal Investigator, Biology
San Diego Supercomputer Center
La Jolla, CA 92093-0505
Tel: 858-822-0866
Fax: 858-822-0866

Research Program:
My research effort is called Next Generation Tools for Biology. Its focus is on creating enabling software tools and infrastructure for Biology and Biomedical Applications. I have crafted a program to take 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 to high end data and computational resources without requiring them to know PERL or SQL. 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 2800 scholarly publications.

Bibliographic Information:
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 brief visit to the private side at Monsanto/Kelco. I was inspired by the use of technology and robotics proposed for the Joint Center for Structural Genomics, and came to SDSC in 2000 to help with the launch of that venture. I have continued to work with goal of using Information Technologies and software in support of Biological/BioMedical research. Before arriving at SDSC, I sampled from many areas of research, including phospholipid and steroid metabolism, eukayotic cell biology, heme enzyme structure:function relationships, and metabolic engineering. My current goal is to see how easy and flexible we can make access to computational resources in the context of a vibrant intellectual community.

Some recent publications are listed here.

The Next Generation Tools for Biology Team:

  • Paul Hoover Senior Software Engineer
  • Terri Liebowitz Senior Software Engineer

Alumni Team Members:

  • Alex Borchers
  • Sasha Buzko
  • Kevin Fowler
  • Zhijie Guan
  • R. Hannes Niedner
  • Rami Rifiaeh
  • Ashton Taylor
  • Roger Unwin
  • Andy Zhang
  • Jeremy Carver Software Engineer
  • Lucie Chan Senior Software Engineer
  • Cassie Graff Intern