Third International Workshop on

Hybrid Systems Biology

Vienna, Austria, July 23-24, 2014
at CAV 2014

 



Location 

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 

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
08.45 - 9.45
 Invited Talk: Calin Guet (IST Austria)
Synthetic Systems Biology
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
10.15 - 10.45 Coffee Break
10.45 - 11.30
 Alexandre Donzé (Berkeley)
Tutorial: Simulation-based Parameter Synthesis in Systems Biology

Special Session: Collaboration with Biologists:
11.30 - 12:00
 J.M. Moulis (LBFA, Grenoble) and Eric Fanchon (TIMC, Grenoble)
Modeling Iron Homeostasis in Mammalian Cells
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
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
13.00 - 14.30 Lunch Break

14:30-16:00 Session 181G - Location: FH, Seminarraum 101A
14.30 - 15:30
 Marco Antoniotti (Univ. of Milano Bicocca)
Tutorial: The Cellular Potts Model
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
16.00 - 16.30 Coffee Break

Thursday, July 24th

08:45-10:15 Session 189B - Location: FH, Seminarraum 101A
08.45 - 9.45
 Invited Talk: David Harel (Weizmann Institute)
The Whole Organism Challenge
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
10.15 - 10.45 Coffee Break

10:45-13:00 Session 191E - Location: FH, Seminarraum 101A
10.45 - 11.30
 Radu Grosu (TU Wien)
Tutorial: Challenges and Opportunities in Controlling the Human Heart
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
12.00 - 12:30
 Charalampos Kyriakopoulos and Verena Wolf (Univ. of Saarland)
Optimal Observation Time Points in Stochastic Chemical Kinetics
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
13.00 - 14.30 Lunch Break

14:30-16:00 Session 193B - Location: FH, Seminarraum 101A
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
14:55 - 15:20
 Anatoly Sorokin, Oksana Sorokina and J. Douglas Armstrong (Univ. of Edinburgh)
RKappa: Statistical Sampling Suite for Kappa Models
15:20 - 16:00
 Oded Maler (Verimag)
Concluding Remarks: Dynamic Systems Biology
16.00 - 16.30 Coffee Break


Scope

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:


Program co-Chairs


Local Organization and Publicity Chair


Program Committee


Steering Committee