This workshop will be devoted to computational support for Systems Biology. Our aim is to bring together people from bioinformatics, computer science and biology.
In particular, we focus on modeling and analysis techniques for various regulatory networks. Examples are genetic regulation, metabolic processes, and signalling pathways within a cell. The interaction between such networks is of special interest.
We welcome presentations on integrated modeling techniques, e.g. using differential equations, or using (probabilistic) discrete models. Furthermore, contributions on scalable analysis methods are welcome, such as system reduction, and model checking techniques, in order to identify crucial properties of (emerging) cell behaviour.
The workshop is organised by the EC-MOAN project, and consists of presentations from people both within and outside the project. There will be plenty of time to discuss in which direction the research field should move.
| 09:00-10:00 | EC-MOAN session 1: Modelling |
| 09:00-09:20 |
Goals and Results of the EC-MOAN project Jaco van de Pol (U Twente, NL) |
| 09:20-09:40 |
Omnipresent two-component signaling governs swift and robust responses even at low molecule numbers Frank J. Bruggeman (VU Amsterdam, NL) |
| 09:40-10:00 |
Modelling ammonium assimilation regulation in Escherichia coli Hongwu Ma (Edinburgh University, UK) |
| 10:00-10:30 | Coffee break |
| 10:30-11:30 | Session: Methodology |
| 10:30-11:00 |
Modelling biochemical pathways with Bio-PEPA and CTMCs Jane Hillston (Edinburgh University, UK) |
| 11:00-11:30 |
Sound identification and model merging when studying type 2 diabetes Gunnar Cedersund (Linköping University, SE) |
| 11:30-12:30 | Session: Stochastic Process Algebra |
| 11:30-11:50 |
Stochastic automata for replication, translation and translesion synthesis Erik de Vink (TU Eindhoven, NL) |
| 11:50-12:10 |
Process algebraic modelling and analysis of signalling pathway crosstalk Robin Donaldson (Glasgow University, UK) |
| 12:10-12:30 |
Modelling scaffold-mediated crosstalk between the cAMP and the Raf-1/MEK/ERK pathways Oana Andrei (Glasgow University, UK) |
| 12:30-14:00 | Lunch break |
| 14:00-15:00 | EC-MOAN session 2: Analysis |
| 14:00-14:20 |
Qualitative analysis of carbon starvation response in E. coli Valentina Baldazzi (INRIA Grenoble, FR) |
| 14:20-14:40 |
On Computational Analysis of Large ODE Models David Safranek (Masaryk University, Brno, CZ) |
| 14:40-15:00 |
Modeling kinase signalling pathways in cells using UPPAAL Rom Langerak (U Twente, NL) |
| 15:00-16:30 | Session: Quantitative Analysis |
| 15:00-15:30 |
A general computational method for robustness analysis with applications to synthetic gene networks Gregory Batt (INRIA Rocquencourt, Fr) |
| 15:30-16:00 |
Executing Multicellular Development:
Quantitative Predictive Modelling of C. elegans Vulva K. Anton Feenstra (VU Amsterdam, NL) |
| 16:00-16:30 |
BioModel Engineering and its role in Systems Biology David Gilbert (Brunel University, UK) |
| 16:30-17:00 | Tea break |
| 17:00-18:00 | Panel Discussion |
Organizers
Frank Bruggeman (VU Amsterdam) and Jaco van de Pol (U Twente)
Co-located with
European Conference on Complex Systems, ECCS 2009