Formal Methods in Systems Biology

This book constitutes the refereed proceedings of the First International Workshop on Formal Methods in Systems Biology, FMSB 2008, held in Cambridge, UK, in June, 2008.

The 9 revised full papers presented were carefully reviewed and selected from the workshop lectures that all were invited contributions. The purpose of this meeting was to identify techniques for the specification, development and verification of biological models. It also focused on the design of tools to execute and analyze biological models that can significantly advance our understanding of biological systems.

Klappentext

Thisvolumecontainstheproceedingsofthe?rstinternationalmeetingonFormal Methods in Systems Biology, held at Microsoft Research, Cambridge, UK, June 4-5, 2008. While there are several venues that cover computational methods in systems biology,there is to date no single conference that brings together the application of the range of formal methods in biology. Therefore, convening such a meeting could prove extremely productive. The purpose of this meeting was to identify techniques for the speci?cation, development and veri?cation of biological m- els.Italsofocusedonthedesignoftoolstoexecuteandanalyzebiologicalmodels in ways that can signi?cantly advance our understanding of biological systems. As a forum for this discussion we invited key scientists in the area of formal methods to this unique meeting. Although this was a one-o? meeting, we are exploring the possibility of this forming the ?rst of what might become an annual conference. Presentations at the meeting were by invitation only; future meetings are expected to operate on a submission and review basis. The Steering Committee and additional referees reviewed the invited papers. Each submission was evaluated by at least two referees. The volume includes nine invited contributions. Formal Methods in Systems Biology 2008 was made possible by the cont- bution and dedication ofmany people. First of all,we wouldlike to thank allthe authors who submitted papers. Secondly, we would like to thank our additional invited speakers and participants. We would also like to thank the members of the Steering Committee for their valuable comments. Finally, we ackno- edge the help of the administrative and technical sta? at the MicrosoftResearch Cambridge lab.

Inhalt

Contributed Papers.- Generic Reactive Animation: Realistic Modeling of Complex Natural Systems.- Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions.- Computational Probability for Systems Biology.- Design Issues for Qualitative Modelling of Biological Cells with Petri Nets.- Combining Intra- and Inter-cellular Dynamics to Investigate Intestinal Homeostasis.- Approximating Continuous Systems by Timed Automata.- From Reaction Models to Influence Graphs and Back: A Theorem.- Rule-Based Modelling, Symmetries, Refinements.- One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II.