ETAPS 2019
Sat 6 - Thu 11 April 2019 Prague, Czech Republic
Sun 7 Apr 2019 16:00 - 16:30 at S9 - Synthesis and Inference Chair(s): Michela Chiappalone

Cell signaling plays an important role in the normal functioning of cells and in health conditions such as cancers and immune diseases. Cell signaling models, capturing the transformations of many different molecular species, are one of the most successful applications of dynamical systems biology. Since they involve highly nonlinear dynamics, the predicting power of these models is often limited due to the difficulty in estimating the relevant kinetic parameters. Fluorescent labeling in conjunction with super-resolution microscopy provides in vivo trajectories of receptors and other bio-molecules of interest. This modality is possibly the most direct source of quantitative information on molecular processes in cells. Unfortunately, it is separated by a few orders of magnitude from the resolution of current quantitative models of cell signaling. Signaling models typically require properties (concentrations, reaction rates) averaged over the entire cell; single particle tracking looks at individual molecules in small fraction of the cell. In principle, the gap in resolution can be bridged using simulations: validate a fully spatial model at SPT resolution, then use a consistent abstraction / averaging procedure to infer effective kinetics on larger spatial scales. Extrapolating diffusion coefficients and dimerization rates observed at SPT resolution is complicated by the presence of spatial structure that interferes with the free movement of molecules of interest. Here we present a method used to identify such structures, based on deviations from ideal Brownian motion and outline a framework aimed at refinement using simulated motion in a known landscape.

Sun 7 Apr

Displayed time zone: Amsterdam, Berlin, Bern, Rome, Stockholm, Vienna change

16:00 - 18:00
Synthesis and InferenceHSB at S9
Chair(s): Michela Chiappalone Italian Institute of Technology
16:00
30m
Talk
Extracting landscape features from single particle trajectories
HSB
Ádám Halász West Virginia University, Ouri Maler West Virginia University, Jeremy S Edwards University of New Mexico
16:30
30m
Talk
Fuzzy Matching in Symbolic Systems Biology
HSB
Adrian Riesco Universidad Complutense de Madrid, Beatriz Santos-Buitrago Seoul National University, Merrill Knapp SRI International, Gustavo Santos-Garcia Universidad de Salamanca, Carolyn Talcott SRI International
17:00
30m
Talk
Data-informed parameter synthesis for population Markov chains
HSB
Matej Hajnal Masaryk University, Tatjana Petrov Universität Konstanz, David Safranek Masaryk University, Morgane Nouvian University of Konstanz
17:30
10m
Day closing
Closing
HSB