Go to the call for papers for the special issue on Information and Computation
Accepted Papers:
- D. Bruce, J.
Whiteley and P. Pathmanathan.
Modelling the effect of gap junctions on tissue-level cardiac electrophysiology - R. Testylier
and T. Dang.
Analysis of parametric biological models - A.
Georgoulas, A. Clark, A. Ocone, S. Gilmore and G. Sanguinetti.
A subsystems approach for parameter estimation of ODE models of hybrid systems - N. Mobilia,
A. Donzé, J.-M. Moulis and E. Fanchon.
A Model of the Cellular Iron Homeostasis Network Using Semi-Formal Methods for Parameter Space Exploration - A.
Casagrande, T. Dreossi and C. Piazza.
Hybrid Automata and epsilon-Analysis on a Neural Oscillator - P. Dluhoš, D.
Šafránek and L. Brim.
On Expressing and Monitoring Oscillatory Dynamics - V. Noel, D.
Grigoriev, S. Vakulenko and O. Radulescu.
Hybrid models of the cell cycle molecular machinery - G. Caravagna,
A. Graudenzi, M. Antoniotti, G. Mauri and A. D'Onofrio.
Effects of delayed immune-response in tumor immune-system interplay - K.G. Larsen,
M. Mikucionis, A. Legay, A. David, S. Sedwards, D. Du and D. Bøgsted
Poulsen.
Statistical Model Checking for Stochastic Hybrid System - L.O. Loohuis,
A. Witzel and B. Mishra.
Cancer Hybrid Automata: Extended Abstract - P. Liò, E.
Merelli and N. Paoletti.
Disease processes as hybrid dynamical systems
Workshop Program
| 09.00 - 09.15 |
Opening Session | |
| 09.15 - 10.00 |
Invited Talk: Radu Grosu Simulating the human heart: the great challenge |
|
Session 1: Heart Modelling |
||
| 10.00 - 10.30 | D. Bruce, J. Whiteley and P.
Pathmanathan. Modelling the effect of gap junctions on tissue-level cardiac electrophysiology |
|
| 10.30 - 11.00 | Coffee Break | |
Session 2: Hybrid systems with Uncertain Parameters |
||
| 11.00 - 11.30 | R. Testylier and T. Dang. Analysis of parametric biological models |
|
| 11.30 - 12.00 | A. Georgoulas, A. Clark, A. Ocone, S.
Gilmore and G. Sanguinetti. A subsystems approach for parameter estimation of ODE models of hybrid systems |
|
| 12.00 - 12.30 | N. Mobilia, A. Donzé, J.-M.
Moulis and E. Fanchon. A Model of the Cellular Iron Homeostasis Network Using Semi-Formal Methods for Parameter Space Exploration |
|
| 12.30 - 14.00 | Lunch | |
Session 3: Abstraction and Analysis |
||
| 14.00 - 14.30 | A. Casagrande, T. Dreossi and C. Piazza. Hybrid Automata and epsilon-Analysis on a Neural Oscillator |
|
| 14.30 -15.00 | P. Dluhoš, D. Šafránek and L. Brim. On Expressing and Monitoring Oscillatory Dynamics |
|
| 15.00 - 15.30 | V. Noel, D. Grigoriev, S. Vakulenko and
O. Radulescu. Hybrid models of the cell cycle molecular machinery |
|
| 15.30 - 16.00 | Coffee Break | |
Session 4: Stochastic Hybrid Modelling |
||
| 16.00 - 16.30 | G. Caravagna, A. Graudenzi, M.
Antoniotti, G. Mauri and A. D'Onofrio. Effects of delayed immune-response in tumor immune-system interplay |
|
| 16.30 - 17.00 | K.G. Larsen, M. Mikucionis, A. Legay, A.
David, S. Sedwards, D. Du and D. Bøgsted Poulsen. Statistical Model Checking for Stochastic Hybrid System |
|
Session 5: Non-deterministic hybrid modelling |
||
| 17.00 - 17.30 | L.O. Loohuis, A. Witzel and B. Mishra. Cancer Hybrid Automata |
|
| 17.30 - 18.00 | P. Liò, E. Merelli and N. Paoletti. Disease processes as hybrid dynamical systems |
|
The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways and cardiac tissues electrophysiology.
This workshop aims at
collecting
scientists working in the
area of hybrid modeling applied to systems biology, in order to discuss
about current achieved goals, current challenges and future possible
developments.
Topics of interest include, but are not limited to:
- Hybrid models of biological systems (case studies of genetic, cellular networks, models of tissues, etc.)
- Models of biological systems with hybrid behavior
- Computational and mathematical analysis techniques for hybrid systems (i.e. reachability, model checking, abstract interpretation, bifurcation theory for hybrid dynamical systems, stability analysis, etc.), with applications in Systems Biology
- Hybrid system identification techniques (learning the model from the experimental data)
- Efficient simulation techniques for hybrid systems
- Hybrid modeling languages for biological systems
- Hybrid systems coping with incomplete and uncertain information
- Hierarchical Hybrid Systems for multi scale analysis
- Stochastic Hybrid Systems
- Hybrid simulation (stochastic/deterministic) methods for biological systems
- Abstraction and Approximation techniques
- Hybrid Systems modeling for Synthetic Biology
- Hybrid Control of biological systems
- Sensitivity analysis for hybrid systems
- Behaviour-driven parameters identification for hybrid systems
- Analysis and simulation tools
We solicit the submission of unpublished results that address on both
theoretical and applied aspects of hybrid modeling techniques in
systems biology. Details about publication of proceedings will be made
available soon.
The proceedings will be published in the Electronic Proceedings in
Theoretical
Computer Science (EPTCS) series. There will be a following
special
issue on Information
and
Computation, based on selected papers of the workshop.
Paper
submission
Full papers should be no more than 15 pages long, typesetted in the EPTCS-style.
Electronic submissions of abstracts and of full-length papers (in PDF
format), can be done
through the online
submission system.
There will be a special issue on Information and Computation, based on selected papers of the workshop.
Registration
The registration can be done via the CONCUR
2012 web site.
Registration is now open. Early registration deadline is August 10, 2012.
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| August 7, 2012 | - | Camera-ready of accepted papers |
- Radu Grosu, TU Wien, Austria
- Ezio Bartocci, TU Wien, Austria
- Luca Bortolussi, Univerity of Trieste, Italy
- Marco Antoniotti, University of Milano Bicocca
- Ezio Bartocci, TU Wien, Austria (co-chair)
- Gregory Batt, INRIA Paris-Rocquencourt, France
- Luca Bortolussi, Univerity of Trieste, Italy (co-chair)
- Alberto Casagrande, University of Trieste, Italy
- Edmund Clarke, Carnegie Mellon, USA
- Thao Dang, VERIMAG Lab, Grenoble, France
- Alexandre Donzé, UC Berkley, USA
- James R. Faeder, University of Pittsburgh, USA
- Jasmin Fisher, Microsoft Research, Cambridge, UK
- Vashti Galpin, University of Edinburgh, UK
- Colas Le Guernic, DGA-MI, France
- Oded Maler, VERIMAG Lab, Grenoble, France
- Emanuela Merelli, University of Camerino, Italy
- Bud Mishra, NYU, USA
- Carla Piazza, University of Udine, Italy
- Alberto Policriti, University of Udine, Italy
- Scott A. Smolka, University of Stony Brook, USA
- Gouhei Tanaka, University of Tokyo, Japan
- Verena Wolf, Saarland University, Germany
- Paolo Zuliani, Carnegie Mellon, USA