Formal Methods in Systems Biology

Formal Methods in Systems Biology

Scope

The purpose of this meeting is to bring researchers together on the application of formal methods to biology. This includes techniques for the specification, development and verification of biological models, as well as the design of tools to execute and analyze biological models.

Topics of interest include (but are not restricted to):

  • Application of formal methods for the construction and analysis of computational models describing various biological processes
  • Tools developed for the design and analysis of biological models
  • Applications of model-checking
  • Synthesis of biological models
  • Relating formally different levels of abstraction
  • Applications of concurrency theory in biology
  • Biologically-inspired advances in formal methods
  • Formal analysis applied to data bases

Important Dates

  • November 8, 2007: Invitations
  • February 15, 2008: Paper submission
  • March 15, 2008: End of review process
  • March 29 , 2008: Final version submission
  • June 4-5, 2008: Meeting dates

Call for Papers

This year all papers are by invitation only.

In addition to the FMSB proceedings volume with Springer Lecture Notes in Bioinformatics (LNBI), Theoretical Computer Science (TCS) will publish a selected set of FMSB contributions in a special issue.

lnbi

Schedule

Wednesday June 4, 2008

 

TIME SPEAKER EVENT
9:00 am Jasmin Fisher Welcoming Remarks
9:30 am David Harel Some Comments on Genericity and Linkage in Modelling Biology
10:30 am Coffee Break
Chair: Satoru Miyano
11:00 am Hillel Kugler “Don’t Care” Modelling Extended
11:30 am Nir Piterman Bounded Asynchrony for Modelling Biological Systems
12.00 pm Verena Wolf Computational Probability for Systems Biology
12:30 pm Lunch
Chair: Marta Kwiatkowska
13:30 pm Christopher Langmead Formal Verification Under Parameter Uncertainty
14:15 pm Daniel Kroening Identification of Glass Networks with Periodic Orbits
15:00 pm Coffee Break
Chair: Amir Pnueli
15:30 pm Satoru Miyano Cell System Markup Language and Cell Illustrator for Systems Biology Computational Platform
16:15 pm Wan Fokkink Design Issues for Qualitiative Modelling of Biological Cells with Petri Nets
18:30 pm Punting
19:30 pm Dinner

 

Thursday June 5, 2008

 

TIME SPEAKER EVENT
Chair: Stephen Emmott
9:00 am Sydney Brenner Keynote Presentation: What is Systems Biology?
10:00 am Coffee Break
Chair: David Harel
10:30 am Luca Cardelli Molecules as Automata
11:15 am Andrew Phillips Improving Modularity of Biological Processes in Stochastic Pi Calculus
11:45 am Marta Kwiatkowska Combining Intra- and Inter-Cellular Dynamics to Investigate Intestinal Homeostasis
12:30 pm Lunch
Chair: Adelinde Uhrmacher
13:45 pm Oded Maler Approximating Continuous Systems by Timed Automata
14:30 pm Francois Fages From Reaction Models to Influence Graphs and Back: Theorem
15:15 pm Coffee Break
Chair: Luca Cardelli
15:30 pm Russell Harmer Rule-Based Modelling of Cellular Signalling
16:15 pm Adelinde Uhrmacher One Modelling Formalism and Simulator is not enough! A Computational Biology Approach Based on James II
17:00 pm Closing Remarks
17:30 Light Dinner

Steering Committee

  • Jasmin Fisher (Chair) – Microsoft Research Cambridge
  • David Harel – Weizmann Institute of Science
  • Stephen Emmott – Microsoft Research Cambridge
  • Amir Pnueli – NYU / Weizmann Institute of Science
  • Claire Tomlin – Stanford / Berkeley
  • Luca Cardelli – Microsoft Research Cambridge
  • Tom Henzinger – EPFL

 

Speakers

Jasmin Fisher (Chair) - Microsoft Research Cambridge

jfisher

Group Leader

Executable Biology, Computational Biology Division, Microsoft Research Cambridge

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Sydney Brenner - Salk Institute

brenner

Professor

Noble prize winner of physiology and medicine, 2002, Salk Institute

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Christopher Langmead - Carnegie Mellon University

clangmead

Assistant Professor

Computer Science Department, Carnegie Mellon University

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Satoru Miyano - Tokyo University

miyano

Professor

Institute of Medical Science, Human Genome Centre, Laboratory of DNA information analysis, Tokyo University

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Nir Piterman - Imperial College London

piterman

Research Fellow

Department of Computing, Imperial College London

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Daniel Kroening - Oxford University

kroning

Lecturer

Computing Laboratory, Oxford University

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Marta Kwiatkowska - Oxford University

kwiatkowska

Professor

Computing Laboratory, Oxford University

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Adelinde Uhrmacher - Rostock University

uhrmacher

Professor

Institute of Computer Science, Rostock University

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Andrew Phillips - Microsoft Research Cambridge

phillips

Group Leader

Programming Languages for Biology, Computational Biology Division, Microsoft Research Cambridge

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Russell Harmer - CNRS Universite Paris-Diderot

harmer

Professor

CNRS, Universite Paris-Diderot

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François Fages - INRIA Paris

fages

Senior Research Scientist

INRIA

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Wan Fokkink - Amsterdam University

fokkink

Professor

Department of Computer Science, Amsterdam University

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Hillel Kugler - Microsoft Research Cambridge

kugler

Group Leader

Systems Biology, Computational Biology Division, Microsoft Research Cambridge

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David Harel - Weizmann Institute of Science

harel

Professor

Computer Science Department, Weizmann Institute of Science

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Luca Cardelli - Microsoft Research Cambridge

cardelli

Principle Director

Programming Languages Group, Microsoft Research Cambridge

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Verena Wolf - EPFL

wolf

Post-doc

School of Computer and Communication Sciences, EPFL Switzerland

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Oded Maler - CNRS - Verimag

images/oMaler.jpg

Research Director

CNRS Verimag

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Confirmed Participants

  • Jasmin Fisher – Microsoft Research Cambridge
  • Sydney Brenner – Salk Institute
  • Robin Milner – Cambridge University
  • Christopher Langmead – Carnegie Mellon University
  • Satoru Miyano – Tokyo University
  • Nir Piterman – Imperial College London
  • Daniel Kroening – Oxford University
  • Marta Kwiatkowska – Oxford University
  • Adelinde Uhrmacher – Rostock University
  • Andrew Phillips – Microsoft Research Cambridge
  • Russell Harmer – CNRS Universite Paris-Diderot
  • François Fages – INRIA Paris
  • Wan Fokkink – Amsterdam University
  • Hillel Kugler – Microsoft Research Cambridge
  • David Harel – Weizmann Institute of Science
  • Luca Cardelli – Microsoft Research Cambridge
  • Stephen Emmott – Microsoft Research Cambridge
  • Amir Pnueli – NYU / Weizmann Institute of Science
  • Tom Henzinger – EPFL
  • Byron Cook – Microsoft Research Cambridge
  • Josh Berdine – Microsoft Research Cambridge
  • John Heath – Birmingham University
  • Michael Huth – Imperial College London
  • Andreas Podelski – Freiburg University
  • Steve McKeever – Oxford University
  • Verena Wolf – EPFL
  • Luke Church – Cambridge University
  • Garth Ilsley – EBI
  • Antje Beyer – Cambridge University
  • Oksana Tymchyshyn – Birmingham University
  • Oded Maler – CNRS – Verimag
  • Yaki Setty – Microsoft Research Cambridge
  • Mike Gordon – Cambridge University
  • Satnam Singh – Microsoft Research Cambridge
  • Ralf Herbrich – Microsoft Research Cambridge
  • Vincent Schachter – CEA France

 

Travel Information

Travel to and from Cambridge is very straightforward with direct trains, buses and easily accessible roads.

The FMSB Meeting will take place at the Microsoft Research Cambridge Lab, a shuttle will be provided to and from the Lab on a daily basis. It will be scheduled to pick up from the Hotel Felix and Hotel du Vin.

Collections from The Felix Hotel on 4th & 5th June 2008

Day 1

  • 8.15am depart from hotel for Microsoft Research Cambridge Lab
  • 5.15pm depart from Microsoft Research for The Felix Hotel
  • 6.10pm depart from The Felix Hotel for St John’s college
  • 10.30pm depart from St John’s College for The Felix Hotel

Day 2

  • 8.20am depart from The Felix Hotel for Microsoft Research Cambridge Lab.

Collections from The Hotel du Vin on 4th & 5th June 2008

Day 1

  • 8.15am depart from hotel for Microsoft Research Cambridge Lab
  • 5.15pm depart from Microsoft Research for The Hotel du Vin
  • 6.10pm depart from The Hotel du Vin for St John’s college
  • 10.30pm depart for The Hotel du Vin

Day 2

  • 8.20am depart from The Hotel du Vin for Microsoft Research Cambridge Lab