Scientific Programming for Biologists (and Everyone Else)

This session at eScience Workshop 2011 includes the following presentations:

  • An Open Source Library for Bioinformatics-Simon Mercer, Microsoft Research
  • Programming with Massive Data Sources Made Simple, Fast, and Error-Free-Don Syme, Microsoft Research

Speaker Details

Dr. Mercer has a background in zoology and has worked in various aspects of bioinformatics over the years. Having managed the development of the Canadian Bioinformatics Resource, a national life science service-provision network in Canada, he worked as Director of Software Engineering at Gene Codes Corporation before moving to the External Research team of Microsoft Research. In his current role as Director of Health and Wellbeing, he manages collaborations between Microsoft and academia in the area of healthcare research. Dr. Mercer’s interests include bioinformatics, translational medicine, and the management of scientific data.

I graduated from the Australian National University in 1993, and joined Microsoft Research in 1998. Before that I was a PhD. student at the University of Cambridge Computer Laboratory http://www.cl.cam.ac.uk. A while ago I spent three months at SRI http://www.csl.sri.com and a six month jaunt at Intel http://www.intel.com. Clearly my ultimate aim is to work for every multinational mega corporation in the computing game, so I’ll throw in links to IBM http://www.ibm.com, Sun http://www.sun.com and Compaq http://www.compaq.com for good measure.
My research interests include the formal modeling of programming languages and abstract machines and techniques for the verification of their properties. Example machines include high level languages defined by operational semantics, stack machines such as the JVM, and hardware devices at various levels of abstraction. Typical properties include correctness (by correlating the machine against a higher-level specification) and type soundness (by proving the preservation of an appropriate invariant, which is implied by a statically checked condition). Typical techniques include model checking, automated reasoning, abstract interpretation and manual declarative proof declare/index.htm.
Since joining MSR I’ve worked extensively with the COM+ team analyzing their code verification mechanism along with Andy Gordon.

Date:
Speakers:
Simon Mercer and Don Syme
Affiliation:
MSRC

    • Portrait of Jeff Running

      Jeff Running

    • Portrait of Simon Mercer

      Simon Mercer