
HSB 2014 will be a two-day satellite workshop of CAV 2014, Conference on Computer-aided Verification, the 26th International which is part of the Vienna Summer of Logic.
Registration fees for a two-days workshop are 200 Euro (regular, by May 20) 240 Euro (late, by June 30, 2014) and 260 Euro (on site). One can register to the HSB Workshop without registering to the CAV conference. A person registered to HSB can attend any parallel Vienna Summer Logic event on the same day. More local information can be found here.
Workshop Program
Wednesday, July 23rd
08:45-10:15 Session 168C - Location: FH, Seminarraum 101A |
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08.45 - 9.45 |
Invited Talk: Calin Guet (IST Austria) Synthetic Systems Biology |
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09.45 - 10.15 |
Donal Stewart, Stephen Gilmore and Michael Cousin (Univ. of Edinburgh) FM-Sim: A Hybrid Protocol Simulator of Fluorescence Microscopy Neuroscience Assays with Integrated Bayesian Inference |
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10.15 - 10.45 | Coffee Break | |
10.45 - 11.30 |
Alexandre Donzé (Berkeley) Tutorial: Simulation-based Parameter Synthesis in Systems Biology |
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Special Session: Collaboration with Biologists: |
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11.30 - 12:00 |
J.M. Moulis (LBFA, Grenoble) and Eric Fanchon (TIMC, Grenoble) Modeling Iron Homeostasis in Mammalian Cells |
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12.00 - 12:30 |
Hidde de Jong (INRIA, Grenoble) and Hans Geiselman (Univ. of Grenoble) The Analysis of Global Regulatory Networks in Bacteria using Models and Experiments |
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12.30 - 13:00 |
Adam Halasz (Univ. of West Virginia) and J.S. Edwards (Univ. of New Mexico) Membrane-bound Receptor Imaging, Data Analysis and Model Building |
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13.00 - 14.30 | Lunch Break | |
14:30-16:00 Session 181G - Location: FH, Seminarraum 101A |
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14.30 - 15:30 |
Marco Antoniotti (Univ. of Milano Bicocca) Tutorial: The Cellular Potts Model |
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15.30 - 16:00 |
Tommaso Dreossi (Univ. of Udine),
Thao Dang (Verimag) and Carla Piazza (Univ. of Udine) Parameter Synthesis using Parallelotopic Enclosure and Applications to Epidemic Models |
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16.00 - 16.30 | Coffee Break |
Thursday, July 24th
08:45-10:15 Session 189B - Location: FH, Seminarraum 101A |
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08.45 - 9.45 |
Invited Talk: David Harel (Weizmann Institute) The Whole Organism Challenge |
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09.45 - 10.15 |
Alvis Brazma (EBI),
Karlis Cerans (LIMCS Riga), Dace Ruklisa (Univ. of London), Thomas Schlitt (Kings College) and Juris Viksna (LIMCS Riga) Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks |
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10.15 - 10.45 | Coffee Break | |
10:45-13:00 Session 191E - Location: FH, Seminarraum 101A |
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10.45 - 11.30 |
Radu Grosu (TU Wien) Tutorial: Challenges and Opportunities in Controlling the Human Heart |
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11.30 - 12:00 |
David C Sterratt,
Oksana Sorokina and J Douglas Armstrong (Univ. of Edinburgh) Integration of Rule-based Models and Compartmental Models of Neurons |
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12.00 - 12:30 |
Charalampos Kyriakopoulos and
Verena Wolf (Univ. of Saarland) Optimal Observation Time Points in Stochastic Chemical Kinetics |
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12.30 - 13:00 |
Alexandre Rocca (TIMC, Grenoble),
Thao Dang (Verimag) and Eric Fanchon (TIMC, Grenoble) Exploiting the Eigenstructures of Linear Systems to Speed up Reachability Computation |
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13.00 - 14.30 | Lunch Break | |
14:30-16:00 Session 193B - Location: FH, Seminarraum 101A |
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14.30 - 14:55 |
Claudio Angione (Univ. of Cambridge),
Ezio Bartocci (TU Wien), Luca Bortolussi (Univ. of Trieste), Pietro Lio' (Univ. of Cambridge), Annalisa Occhipinti (Univ. of Cambridge) and
Guido Sanguinetti (Univ. of Edinburgh) Bayesian Design for Whole Cell Synthetic Biology Models |
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14:55 - 15:20 |
Anatoly Sorokin, Oksana Sorokina and J. Douglas Armstrong (Univ. of Edinburgh) RKappa: Statistical Sampling Suite for Kappa Models |
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15:20 - 16:00 |
Oded Maler (Verimag) Concluding Remarks: Dynamic Systems Biology |
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16.00 - 16.30 | Coffee Break |
Systems biology aims at providing a system-level understanding of biological systems by unveiling their structure, dynamics, and control methods. Living systems are intrinsically multi-scale in space, in organization levels and in time; they also exhibit a mixture of deterministic and stochastic behaviors. It is therefore very difficult to model them in a homogeneous framework, for instance, by systems of differential equations or by discrete-event systems. Furthermore, such models are often not easily amenable to formal analysis and their simulations at the organ or even the cell level are frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale-up well for both simulation and formal analysis of biological processes.
Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology. They have been applied to successfully capture the behavior of several biological complex systems, including genetic regulatory networks, metabolic reactions, signaling pathways as well as higher level models of tissues and organs. As the challenges of scale and intrinsic inhomogeneity are coming to the forefront of systems biology efforts, they highlight the value of a hybrid dynamical modeling paradigm that integrates mathematical models that address distinct spatio-temporal scales and subsystems.
In this spirit, the scope of the HSB workshop is the general area of dynamical
models in Biology with an emphasis on hybrid approaches, which are not
restricted to a narrow class of mathematical models, and which take
advantage of techniques developed separately in different sub-fields.
Topics of interest include, but are not limited to:
- Models of metabolic, signaling, and genetic regulatory networks in living cells
- Models of tissues, organs; physiological models
- Biological applications of analysis techniques such as reachability computation, model checking, abstract interpretation, bifurcation theory, stability and sensitivity analysis
- Parametric and non-parametric system identification techniques (learning models from experimental data)
- Efficient techniques for combined (stochastic/deterministic, spatial/non-spatial) simulations for biological models
- Modeling languages for biological systems; analysis and simulation tools
- Models coping with incomplete and uncertain information; stochastic hybrid systems
- Hierarchical systems for multi-scale analysis
- Abstraction, approximation and model reduction techniques
- Modeling for synthetic biology and control of biological systems
- Ádám Halász, West Virginia University, USA
- Oded Maler, VERIMAG/CNRS, Grenoble, France
Local Organization and Publicity Chair
- Ezio Bartocci, Vienna University of Technology, Austria
- Marco Antoniotti, University of Milano Bicocca, Italy
- Ezio Bartocci, Vienna University of Technology, Austria
- Gregory Batt, INRIA Rocquencourt, France
- Luca Bortolussi, Univerity of Trieste, Italy
- Thao Dang, VERIMAG/CNRS, Grenoble, France
- Vincent Danos, CNRS/Université Paris-Diderot, France
- Hidde de Jong, INRIA Grenoble - Rhône-Alpes, France
- Alexandre Donzé, UC Berkley, USA
- François Fages, INRIA Rocquencourt, France
- Eric Fanchon, TIMC-IMAG Laboratory, Grenoble, France
- Hans Geiselmann, University of Grenoble, France
- Radu Grosu, Vienna University of Technology, Austria
- Ádám Halász, West Virginia University, USA - (co-chair)
- Thomas Henzinger, IST, Austria
- Jane Hillston, University of Edinburgh, UK
- Agung Julius, Rensselaer Polytechnic Institute, USA
- Heinz Koeppl, ETH Zurich, Switzerland
- Hillel Kugler, Microsoft Research, UK
- Marta Kwiatkowska, Oxford University, UK
- Pietro Lio, University of Cambridge, UK
- Oded Maler, VERIMAG/CNRS, Grenoble, France - (co-chair)
- Bud Mishra, NYU, USA
- Chris Myers, University of Utah, USA
- Casian Pantea, West Virginia University, USA
- Carla Piazza, University of Udine, Italy
- David Šafránek, Masaryk University, Czech Republic
- Ricardo Sanfelice, University of Arizona, USA
- P.S. Thiagarajan, National University of Singapore, Singapore
- Verena Wolf, Saarland University, Germany
- Ezio Bartocci, Vienna University of Technology, Austria
- Luca Bortolussi, Univerity of Trieste, Italy
- Thao Dang, VERIMAG/CNRS, Grenoble, France
- Ádám Halász, West Virginia University, USA
- Oded Maler, VERIMAG/CNRS, Grenoble, France
- Carla Piazza, University of Udine, Italy