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Formal Methods in Systems Biology

First International Workshop, FMSB 2008, Cambridge, UK, June 4-5, 2008, Proceedings

  • Conference proceedings
  • © 2008

Overview

Editors:
  1. Jasmin Fisher
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 5054)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: FMSB 2008.

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Table of contents (9 papers)

  1. Front Matter

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  2. Contributed Papers

    1. Generic Reactive Animation: Realistic Modeling of Complex Natural Systems

      • David Harel, Yaki Setty
      Pages 1-16

    2. Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions

      • Jasmin Fisher, Thomas A. Henzinger, Maria Mateescu, Nir Piterman
      Pages 17-32

    3. Computational Probability for Systems Biology

      • Werner Sandmann, Verena Wolf
      Pages 33-47

    4. Design Issues for Qualitative Modelling of Biological Cells with Petri Nets

      • Elzbieta Krepska, Nicola Bonzanni, Anton Feenstra, Wan Fokkink, Thilo Kielmann, Henri Bal et al.
      Pages 48-62

    5. Combining Intra- and Inter-cellular Dynamics to Investigate Intestinal Homeostasis

      • Oksana Tymchyshyn, Marta Kwiatkowska
      Pages 63-76

    6. Approximating Continuous Systems by Timed Automata

      • Oded Maler, Grégory Batt
      Pages 77-89

    7. From Reaction Models to Influence Graphs and Back: A Theorem

      • François Fages, Sylvain Soliman
      Pages 90-102

    8. Rule-Based Modelling, Symmetries, Refinements

      • Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine
      Pages 103-122

    9. One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II

      • Adelinde M. Uhrmacher, Jan Himmelspach, Matthias Jeschke, Mathias John, Stefan Leye, Carsten Maus et al.
      Pages 123-138

  3. Back Matter

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  1. Formal Methods in Systems Biology

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About this book

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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