LZI - Schloss Dagstuhl - Talks + Materials of Seminar 09091

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Seminar 09091
Formal Methods in Molecular Biology

Rainer Breitling (University of Groningen, NL), David Roger Gilbert (Brunel University, GB), Monika Heiner (BTU Cottbus, D), Corrado Priami (Università di Trento, I)

Seminar Wide Materials

Executive Summary of Dagstuhl Seminar on Formal Methods in Molecular Biology (09091)

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M. Tauqeer Alam , Groningen

Heike Assmus , MPI für Molekulare Pflanzenphysiologie

Johnrob Y. Bantang , LMU München

Developing a projective Brane Calculus based on Activate, Bud and Mate primitive Actions

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Gregory Batt , INRIA - Le Chesnay

Alexander Bockmayr , FU Berlin

Constraint-based analysis of regulatory networks

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Nicola Bonzanni , VU University Amsterdam

Executing multi-cellular development: Petri net model of AC/VU differentiation in C. elegans

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Rainer Breitling , University of Groningen

Frank J. Bruggeman , CWI - Amsterdam

Luca Cardelli , Microsoft Research UK - Cambridge

Molecules as Automata

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Federica Ciocchetta , University of Edinburgh

Modelling the NF-kappaB pathway in Bio-PEPA

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Modelling and analysis of the NF-kappaB pathway in Bio-PEPA

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Maria Pamela C. David , LMU München

Andrea Degasperi , University of Glasgow

Finn Drablos , Univ. of Science & Technology - Trondheim

Analysing eukaryote gene regulation: in vivo, in vitro, in silico, and back again

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Wan Fokkink , Vrije Universiteit Amsterdam

Anna Gambin , University of Warsaw

JAK/STAT pathway activation mechanism model selection via sensitivity analysis

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David Roger Gilbert , Brunel University

BioModel Engineering: Its role in Systems Biology and Synthetic Biology

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Simon Hardy , Mount Sinai Medical School - New York

Analysis of Signal Propagation and Crosstalk within Signaling Networks Using Animated Graph Representations of Dynamical Systems

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Sampsa Hautaniemi , University of Helsinki

On the Use of NF-kB Pathway Petri Net Model

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Data Integration in Systems Biology

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John K. Heath , University of Birmingham

Composing and Decomposing Biological Models

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Monika Heiner , BTU Cottbus

My Petri Net Pictures Book

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Domitille Heitzler , INRIA - Le Chesnay

Dynamic model of FSH signalling pathways in Sertoli cells adapted to two stages

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Jane Hillston , University of Edinburgh

The Bio-PEPA project

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Mathias John , Universität Rostock

Andrzej M. Kierzek , University of Surrey

Constraint based modelling of eukaryotic cell cycle dynamics.

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Ina Koch , MPI for Molecular Genetics / TU Berlin

Searching for New Therapies for Duchenne Muscular Dystrophy through Modeling of Gene Regulation - a Petri Net Approach

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Elzbieta Krepska , Vrije Universiteit Amsterdam

Executing multi-cellular development: Petri Nets Model of the C.elegans Vulva

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Celine Kuttler , University of Lille

Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

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Marek Kwiatkowski , University of Edinburgh

The Continuous pi-Calculus

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Cedric Lhoussaine , University of Lille

The Attributed Pi-Calculus

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Wolfgang Marwan , MPI - Magdeburg

The molecular basis of behavioural plasticity: phototaxis of Halobacterium as case study for extended stochastic Petri nets

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Hiroshi Matsuno , Yamaguchi University

Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm

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Carsten Maus , Universität Rostock

Eduardo Mendoza , LMU München

Algorithmic vs. Equation-based, executable vs. mathematical - is there a middle ground for modelers?

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Satoru Miyano , University of Tokyo

In Silico Pipeline for Extracting Dynamic Transcriptional Networks

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Joachim Niehren , INRIA Lille - North Europe

Alberto Policriti , Università di Udine

Corrado Priami , Microsoft Research - University Trento

Haluk Resat , Pacific Northwest National Lab.

Biological models based on experimental observations

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Alessandro Romanel , Microsoft Research - University Trento

Analyzing various models of Circadian Clock and Cell Cycle coupling

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David Safranek , Masaryk University

On Model-checking a class of ODE models with BioDiVinE

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Torsten Schaub , Universität Potsdam

Detecting Inconsistencies in Large Biological Networks with Answer Set Programming

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Heike Siebert , FU Berlin

Deriving behavior of discrete regulatory networks from subnetwork dynamics

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Sylvain Soliman , INRIA Le Chesnay

P.S. Thiagarajan , National University of Singapore

Approximating Bio-Pathways Dynamics

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Denis Thieffry , Université de la Méditerrannée - Marseille

Compositional logical modelling of molecular regulatory networks

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Jerzy Tiuryn , University of Warsaw

Elucidating Regulatory Mechanisms Downstream of a Signaling Pathway Using Informative Experiments

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Adelinde M. Uhrmacher , Universität Rostock

Cristian Versari , University of Bologna

Stochastic modelling of cellular growth and division by means of the pi@ calculus

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Juris Viksna , University of Latvia

Finite state linear model (FSLM) and analysis of dynamics of gene regulatory networks

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Simon Youssef , LMU München

Liying Yu , University of Groningen

Gianluigi Zavattaro , University of Bologna

On the Turing (in)completeness of Chemical Kinetics

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Seminar 09091 Formal Methods in Molecular Biology

Copyright

Seminar 09091
Formal Methods in Molecular Biology