HSCB 2009

Hybrid Systems Approaches to Computational Biology

A Satellite Workshop of HSCC 2009

April 16, 2009, San Francisco, USA

The registration for the workshop will be available through the registration for the CPSWeek.


Invited (Confirmed) Speakers

Workshop Email

hscb2009 AT gmail.com

Workshop Organizers (Chairs)

Calin Belta
15 Saint Mary's Street, Room 144
Boston University, Brookline, MA 02446
Phone: office: (617) 353 9586, lab: (617) 353 1001 FAX: (617) 353 5548
E-mail: cbelta at bu dot edu
Radu Grosu
Department of Computer Science
State University of New York at Stony Brook
Stony Brook, NY 11794-4400, USA
Office: 1425 CS Building
Tel.: +1 (631) 632-9801
Fax: +1 (631) 632-8334
E-mail: grosu AT cs DOT sunysb DOT edu


Ezio Bartocci
Department of Mathematics and Computer Science
University of Camerino, Italy

Aim: The use of hybrid systems in computational biology has a threefold motivation. First, hybrid-system models unify traditional purely continuous models, such as systems of differential equations capturing the time-evolution of species concentrations, and purely discrete models, such as Boolean networks that capture species interactions. Second, hybrid systems can capture the dynamics of biological networks in which "continuous" processes, such as gene expression, interact with "discrete" events, such as the binding of a transcription factor to the promoter region of a gene. Third, as a unifying framework for control theory and computer science, hybrid systems leverage concepts and tools from both areas, which can be used to specify, analyze, verify, and control the behavior of biological networks.

In this workshop, we will discuss a broad spectrum of fundamental issues in hybrid systems approaches to biology, ranging from the identification of hybrid models from experimental data, to the simulation and formal verification of such models. The covered mathematical models will increase in complexity from piece-wise affine models in discrete and continuous time, to hybrid automata and stochastic hybrid automata, and to spatio-temporal models capturing Brownian motion in 3D virtual cells. We will present techniques for inferring temporal logic properties of such models from simulation and experimental traces. We will discuss abstraction and iterative refinement techniques allowing for the formal verification of the models. For identification, we will present techniques for both stochastic and deterministic models. Finally, we will look into the challenging problem of understanding and synthesize the behavior of large populations of locally interacting cells, whose dynamics are modeled by hybrid automata.

Expected outcomes: The goals of the workshop are to:

  • provide a review of state-of- the-art techniques in hybrid systems approaches to computational biology,
  • identify the main challenges in scalability, verifiability, and controllability of hybrid models of biological systems
  • address the main challenges in the applicability of these techniques to real biological systems.

Organization: The workshop will consist of talks given by the invited speakers listed above and a panel discussion. Each talk will be allocated 40 min, with 30 min for the presentation and 10 min for discussions. The workshop will open with a welcome message and overview of the workshop by the organizers. There will be two ten-minute coffee breaks and a one-hour lunch break. The topic of the panel discussion will be "Bridging the gap between computation and experiments in systems biology".

History: The previous edition of the workshop, Hybrid Systems Biology, took place in San Diego on 12 December 2006 as a satellite event of 45. th. IEEE Conference on Decision and Control. It was organized by Giancarlo Ferrari-Trecate and John Lygeros.