BIBM Workshop on Software Science for System Biology and Bioinformatics

Computational methods in systems biology and bioinformatics have been dominated by the development of algorithms and tools including those for sequence alignments, likelihoods of being a coding region, quantification of microarray data, and structure prediction.   While highly useful and quite often producing significant biologic insights, it is typically not clear how to establish the soundness and accuracy of such tools. This workshop asks how faithful these software tools are to the underlying biology they model? Current approaches tend to rely on a “black box” view of such bioinformatics software systems and tools: how do we construct algorithms, tools and techniques that are, to borrow a phrase from software engineering, correct-by-construction?

The workshop on Software Science in System Biology and Bioinformatics is aimed at highlighting efforts to develop computational systems and models of biological processes where the emphasis is on the ability of the user to reason about the results. Examples would include the development of domain specific languages where the language constructs are designed to mirror the process being simulated; the use of grammatical models such as a term-rewriting grammar to predict polymer structure or chemical reactions; and the development of methods that would extract and test human-understandable rules from trained machine learning automata.

For more information, please contact the workshop organizers:

Robert W. Harrison, Ph.D (Georgia State University) rharrison@cs.gsu.edu

William L. Harrison, Ph.D (University of Missouri) harrisonwl@missouri.edu