CSG 260 Advanced Software Development

Tools for Systems Biology

Why Systems Biology?

Because I spent my sabbatical 2005/2006 at Novartis in the Systems Biology group, we will choose tools for Systems Biology as application domain. Systems biology models the quantitative and simultaneous integration of different biological components and their relationships with one another. Systems biology is a very promising and exciting area of research.

In previous incarnations of this course we focussed on applications in computer science. It is refreshing to learn about a new application domain and to make contributions there.

Systems Biology is a big area and we will focus on reasoning under uncertainty. Normally, if a system is constrained by a set of constraints, all constraints must hold in a model. In biology (and other applications), we are not sure that all constraints must hold, i.e., the system may be contradictory. To cope with uncertainty, we assign a positive weight to each constraint that indicates its importance. Instead of satisfying all constraints, we look for a model that satisfies as many constraints as possible.