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Programme
The preliminary programme.
This site will be continously updated.
Bernsteinsaal = Amber Hall
Salon "Muschel" = Salon "Shell"
Raum "Kranich" = Room "Crane"
12. October 2008 - 15. October 2008
CMSB / Overview
| Time | Tutorial day 12 October | invited talks/posters 13 october | CMSB presentations 14 october | CMSB presentations 15 october | |
|---|---|---|---|---|---|
| 8:30 | registration open | ||||
| 9:00 |
| qualitative modelling of bacterial regulatory networks | signal transduction and metabolism of halophilic archaea: testcases for systems biology | session on simulation methods | |
| 9:30 | |||||
| 10:00 | integrated analysis from abstracts stochastic process algebra | ||||
| 10:30 | coffee | | coffee | coffee | |
| 11:00 | automated proteome-wide determination and modeling of subcellular location | coffee | session on modelling approaches | session on model checking | |
| 11:30 | an exact Brownian dynamics method for cell simulation | ||||
| 12:00 | |||||
| 12:30 | lunch | lunch | lunch | lunch | |
| 13:00 | |||||
| 13:30 | |||||
| 14:00 | multiscale modeling of synaptic signalling | session on process algebra | session on flux analysis | ||
| 14:30 | |||||
| 15:00 | coffee | ||||
| 15:30 | coffee | coffee | coffee | coffee | |
| 16:00 | modeling of common biological patterns in MATLAB and SimBiology | session short talks on selected posters | session on analysis approaches | session on applications | |
| 16:30 | |||||
| 17:00 | poster presentation & Arenas | ||||
| 17:30 | | ||||
| 18:00 | |||||
| 18:30 | |||||
| 19:00-22:00 | extra social event | social event | |
12 October 2008 - Sunday
Tutorial
| time | location | ||
|---|---|---|---|
| 08:30-09:00 | Registration | | Foyer "Muschel" |
| 09:00-10:30 | Tutorial Details | Corrado Priami. Algorithmic Systems Biology | Salon "Muschel" |
| 10:30-11:00 | Coffee Break | | Foyer "Seestern" |
| 11:00-12:30 | Tutorial Details | Robert F. Murphy. Automated Proteome-Wide Determination and Modeling of Subcellular Location | Salon "Muschel" |
| 12:30-13:30 | Lunch | | Room "Kranich" |
| 14:00-15:30 | Tutorial Details | Andrew Phillips. A Visual Programming Language for Biological Processes | Salon "Muschel" |
| 15:30-16:00 | Coffee Break | | Foyer "Seestern" |
| 16:00-17:30 | Tutorial Details | Eckhard Lehmann and Julia Birkenseher. Modeling of common biological patterns in MATLAB and SimBiology | Salon "Muschel" |
| | | ||
| 19:00-22:00 | Extra Social Event | pub crawl | City of Rostock, Restaurant "Alter Fritz" |
13 October 2008 - Monday
Invited Talks / Poster Day /Arenas
| time | location | ||
|---|---|---|---|
| 09:00-10:00 | Chair: Carolyn Talcott | Hidde de Jong INRIA, Rhone Alpes FRA Qualitative Modelling of Bacterial Regulatory Networks | Bernsteinsaal |
| 10:00-11:00 | Jane Hillston University of Edinburgh GBR Integrated analysis from abstracts stochastic process algebra | Bernsteinsaal | |
| 11:00-11:30 | Coffee Break | | Foyer "Bernsteinsaal" |
| 11:30-12:30 | Chair: Adelinde Uhrmacher | Koichi Takahashi The Molecular Sciences Institute USA An exact Brownian Dynamics method for cell simulation | Bernsteinsaal |
| 12:30-13:30 | Lunch | | Restaurant Hotel "Neptun" |
| 14:00-15:00 | Chair: Ursula Kummer | Nicolas Le Novere European Bioinformatics Institute, Hinxton/Cambridge GBR Multiscale modeling of synaptic signalling | Bernsteinsaal |
| 15:00-16:00 | Coffee Break | | Foyer "Bernsteinsaal" |
| 16:00-17:00 | Selected Posters - Short Talks Chair: Francois Fages | 16:00-16:15 Sarala Dissanayake, Matt Halstead and Poul Nielsen Visualization of CellML Models 16:15-16:30 Sayed-Amir Marashi and Alexander Bockmayr Revisiting Flux Coupling Analysis 16:30-16:45 Marit S. Bratlie, Jostein Johansen and Finn Drablos Why do bacterial genes form operons? 16:45-17:00 Xin Lai, Julio Vera Gonzalez, and Olaf Wolkenhauer Use of sensitivity analysis to detect critical biochemical processes in a mathematical model linking intracellular and cell population dynamics in erythropoiesis. | Bernsteinsaal |
| 17:00-18:30 | Posters, and Arenas | Bernsteinsaal & Foyer "Bernsteinsaal" |
14 October 2008 - Tuesday
CMSB Presentations
| time | location | ||
|---|---|---|---|
| 08:45-09:00 | Welcome | | Bernsteinsaal |
| 09:00-10:30 | Chair: Wolfgang Marwan | Dieter Oesterhelt Max Planck Institute of Biochemistry Martinsried GER Signal transduction and metabolism of halophilic archaea: testcases for systems biology | Bernsteinsaal |
| 10:30-11:00 | Coffee Break | | Foyer "Bernsteinsaal" |
| 11:00-12:30 | Session: Modelling Approaches Chair: Hidde de Jong | 11:00-11:30 Ritesh Krishna and Shuixia Guo. A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data 11:30-12:00 Alexander Ullrich and Christoph Flamm. Functional evolution of ribozyme-catalyzed metabolisms in a graph-based Toy-universe 12:00-12:30 Carsten Maus. Component-based Modelling of RNA Structure Folding | Bernsteinsaal |
| 12:30-13:30 | Lunch | | Restaurant Hotel "Neptun" |
| 14:00-15:30 | Session: Process Algebra Chair: Jane Hillston | 14:00-14:30 Michael D. Pedersen and Gordon Plotkin. A Language for Biochemical Systems 14:30-15:00 Mathias John, Cedric Lhoussaine, Joachim Niehren and Adelinde Uhrmacher. The Attributed Pi Calculus 15:00-15:30 Marek Kwiatkowski and Ian Stark. The Continuous pi-Calculus: A Process Algebra for Biochemical Modelling | Bernsteinsaal |
| 15:30-16:00 | Coffee Break | | Foyer "Bernsteinsaal" |
| 16:00-17:30 | Session: Analysis Approaches Chair: Alexander Bockmayr | 16:00-16:30 Dirk Lebiedz, Dominik Skanda and Marc Fein. Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems 16:30-17:00 Pei Ye, Radu Grosu, Scott Smolka and Emilia Entcheva. Formal Analysis of Abnormal Excitation in Cardiac Tissue 17:00-17:30 Laurence Loewe and Jane Hillston. The distribution of mutational effects on fitness in a simple circadian clock | Bernsteinsaal |
| 19:00-22:00 | Social Event | Boat trip to City of Rostock Dinner | |
15 October 2008 - Wednesday
CMSB Presentations
| time | location | ||
|---|---|---|---|
| 09:00-10:30 | Session: Simulation Methods Chair: Koichi Takahashi |
09:00-09:30 Dagmar Köhn and Nicolas Le Novere SED-ML - An XML Format for the Implementation of the MIASE Guideline 09:30-10:00 Lorenzo Dematte, Tommaso Mazza On Parallel Stochastic Simulation of Diffusive Systems 10:00-10:30 Matthias Jeschke, Roland Ewald Large-Scale Design Space Exploration of SSA | Bernsteinsaal |
| 10:30-11:00 | Coffee Break | | Foyer "Bernsteinsaal" |
| 11:00-12:30 | Session: Model Checking Chair: Monika Heiner | 11:00-11:30 Edmund Clarke, James Faeder, Leonard Harris, Christopher Langmead, Axel Legay and Sumit Jha Statistical Model Checking in BioNetGen: Applications to the automated analysis of T-Cell Receptor Signaling Pathway 11:30-12:00 Aurelien Risk, Gregory Batt, Francois Fages and Sylvain Soliman On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology 12:00-12:30 Robin Donaldson and David Gilbert A Model Checking Approach to the Parameter Estimation of Biochemical Pathways | Bernsteinsaal |
| 12:30-13:30 | Lunch | | Restaurant Hotel "Neptun" |
| 14:00-15:30 | Session: Flux Analysis Chair: David Gilbert | 14:00-14:30 Michael D. Pedersen Compositional definitions of minimal flows in Petri nets 14:30-15:00 Abdelhalim Larhlimi and Alexander Bockmayr On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network 15:00-15:30 Markus Durzinsky, Annegret Wagler and Robert Weismantel A combinatorial approach to reconstruct Petri nets from experimantal data | Bernsteinsaal |
| 15:30-16:00 | Coffee Break | | Foyer "Seestern" |
| 16:00-17:30 | Session: Applications Chair: Finn Drablos | 16:00-16:30 Ashish Tiwari and Carolyn Talcott Analyzing a Discrete Model of Aplysia Central Pattern Generator 16:30-17:00 Dragan Bosnacki, Huub ten Eikelder, Marvin N. Steijaert and Erik de Vink Stochastic Analysis of Amino Acid Substitution in Protein Synthesis 17:00-17:30 Richard van der Wath and Pietro Lio' A stochastic single cell based model of BrdU measured Hematopoietic stem cell kinetics | Bernsteinsaal |
| 17:30-17:45 | closing remarks |
Conference started
CMSB 2008