Formal Methods in Systems Biology: First International Workshop, FMSB 2008, Cambridge, UK, June 4-5, 2008, Proceedings
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.
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Realistic Modeling of Complex Natural Systems
Concurrency for Modeling CellCell Interactions
Computational Probability for Systems Biology
Design Issues for Qualitative Modelling of Biological Cells with Petri Nets
Combining Intra and Intercellular Dynamics to Investigate Intestinal Homeostasis
Approximating Continuous Systems by Timed Automata
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abstraction activates ambient analysis animated front-end applied approach automata automaton behavior biochemical Bioinformatics biological models biological systems bounded asynchrony cascade cell cycle cellular chemical reactions clock complex components concurrent conﬁguration crypt CTMC cube deﬁned Deﬁnition described diﬀerent diﬀerential inﬂuence graph dynamical systems eﬀect eﬃcient elegans vulval development equations example execution ﬁrst gene Harel Heidelberg Henzinger hybrid implementation inhibits initial interactions interleaving JAMES II kinetic expressions Kronecker Kronecker product li(B LNBI LNCS macro-step Markov Markov chains matrix mechanism methods Microsoft Research model checking modelling and simulation modelling formalisms molecular molecules networks pathway Petri net Petri nets plugins processes protein reachable reaction model reaction rules reactive animation reﬁnement ri(B scenario-based semantics signiﬁcant simulation algorithms space species speciﬁcation Springer statecharts stem cells stiﬀ stochastic simulation structure sub-volumes syntactical inﬂuence graph Systems Biology techniques theorem tion tool trajectory transition transition relation variable Wnt signalling