Hybrid Systems Study Group

BioHybridControl Group – Hybrid Systems Theory for Biology – Summer 2005

Meeting Time:

For the Summer Session 2005, the meetings are scheduled on Mondays at 4:00pm in 337 Cory.

Purpose:

Recently the research community has seen a lot of effort in the field of Systems Biology. Topics like gene-to-gene regulatory networks, gene-to-protein interactions, noise interaction and exploitation, or molecular-level behavior have gained much understanding from the application of mathematical models which Control Engineers or Mathematicians are rather familiar with.

Specifically, Hybrid Systems appear to be a natural framework to model these systems with, because in nature continuous-time evolutions is often torn apart by the happening of discrete events.

Furthermore, stochasticity seems to be a requirement and a leit-motif in natural evolution.

These observations have led us to investigating possible applications of (Stochastic) Hybrid Systems models to the field of biology.

The group will be of course open to more general applications of System Engineering techniques to the field of molecular biology, as well as integrative biology.

Reading Schedule and Additional Material:

Date	Paper or Topic of Discussion
Upcoming	Joshi, K. Neogi, N., and W. Sanders Dynamic Partitioning of Large Discrete Event Biological Systems for Hybrid Simulation and Analysis
Upcoming	H. McAdams, A. Arkin Simulation of Prokaryotic Genetic Circuits
Upcoming	Denise M. Wolf, Adam P. Arkin 15 Minutes of fim: Control of Phase Variation in E. coli
Upcoming	R. Ghosh, A. Tiwari, and C. Tomlin Automated Symbolic Reachability Analysis with Application to Delta-Notch Signaling Automata
June 3, 2005	*Phoebus Chen* (UCB EECS) will continue with the second part of the MCB primer.
May 27, 2005	*Phoebus Chen* (UCB EECS) will give an MCB primer on the following topics: 'Overview of Transcription and Translation' and 'Example Mechanisms for Transcription Control' [slides] [index]
May 20, 2005	Alur, Belta, Ivancic, Kumar, Mintz, Pappas, Rubin, Schug Hybrid Modeling and Simulation of Biomolecular Networks
May 13, 2005	C. Belta, P. Finin, L.C.G.J.M. Habets, A. Halasz, M. Imielinski, V.Kumar, H. Rubin Understanding the bacterial stringent response using reachability analysis of hybrid systems
May 7, 2005	Lincoln, P. and Tiwari, A. Symbolic systems biology: Hybrid modeling and analysis of biological networks
May 7, 2005	H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, J. Geiselmann Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach
April 29, 2005	More on Stochastic Resonance
April 22, 2005	L. Gammaitoni, et al. Stochastic resonance J.E. Levin, J.P. Miller Broadband neural encoding in the cricket cercal sensory system enhanced by stochastic resonance J.K. Douglass, et al. Noise Enhancement of information transfer in crayfish mechanoreceptors by stochastic resonance D. F. Russell, et al. Use of behavioural stochastic resonance by paddle fish for feeding
April 21, 2005	Cory 285 – 2.00-3.30 – Ronojoy Ghosh (Stanford) will be lecturing on “Hybrid Models for Biology”.
April 1, 2005	H.H. McAdams, A. Arkin Stochastic mechanisms in gene expression C.V. Rao, D. Wolf, A. Arkin Control, exploitation and tolerance of intracellular noise
March 18, 2005	D.T. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions
March 9, 2005	D. Wolf, A. Arkin Motifs, modules and games in bacteria
March 4, 2005	J. Makin and B. Zhu will be leading a discussion on the research topic “Cortical-basal-thalamic loops” Reference paper: S. Narajanan The role of cortico-basal-thalamic loops in cognition: a computational model and preliminary results
February 23, 2005	J. Hu, W.-C. Wu and S. Sastry *Modeling Subtilin Production in Bacillus subtilis* Using Stochastic Hybrid Systems**
February , 2005	Shai Refzen will be presenting on the topic “Dynamics, Templates and Modules of Cockroaches”
Fall 2004
	W.J. Blake, M. Kaern, C.R. Cantor, J.J. Collins Noise in eukaryotic gene expression
	F.Isaacs, J. Hasty, C.R. Cantor, J.J. Collins Prediction and Measurement of an autoregulatory genetic module
	J. Hasty, J. Pradines, M. Dolnik, J.J. Collins Noise-based switches and amplifiers for gene expression

Additional Links:

Biospice Project: www.biospice.org

Some links to Molecular Biology Glossaries: Hedgehog Signaling Glossary
Molecular Cell Biology. Table of Contents
EverythingBio.com

Computational Biology at UCB: www.computationalbiology.berkeley.edu

“Molecular Cell Biology”, by Lodish et. al. (5^th ed.) - book’s on-line resources.

Contact:

For further information about schedule, material, objectives, or questions regarding the website, please get in touch with:

Alessandro Abate (aabate AT eecs DOT berkeley DOT edu)

Last modified: May 31^ts, 2005