W1 "Conclusions despite uncertainties"

Systems biology is a rapidly growing field, which has as its key component to integrate mathematical modelling as an analysis tool for biological data. Mathematical modelling has been used extensively in many other fields, but the application to systems biology raises some new challenges, which warrants the development of new and modified theoretical methods and modelling strategies. This workshop is devoted to one such challange: how to draw conclusions despite the many uncertainties.

Data uncertainty and large mechanistically based models leads to practical unidentifiability, and this leads to the need for a differentiation of those parts of a model that can be validated/trusted (core predictions), and those parts of the model that are more or less arbitrarily uncertain because they cannot be checked by current data. This differentiation can be obtained in different ways, but we will consider at least the following options:

The workshop will be informal, and will consist of both lectures, joint discussions, and group discussions. The intention is to both share ideas and explore new directions, but also to sort out technical details on specific problems, and to discuss general strategies for how to do modelling, and how to not do modelling. Since this might be of general interest also to a wider audience, we might produce a meeting document, which can be published in one form or another.

With the hope of an interesting time in Linköping in June!

Email with practical info and papers to read as background (link)

Preliminary Schedule

Saturday June 19

Session on Optimization-based approaches and direct searches among the ODE-parameters
9.15-9.30 Welcome, introduction to the workshop
9.30-10.00 Gunnar Cedersund*, Linköping, Sweden, "Core-predictions - i.e. shared properties among all acceptable parameters - extends conclusive modelling beyond hypothesis testing"(background papers, 1 and 2)
10.00-10.30 Clemens Kreutz* (Andreas Raue, Jens Timmer), Freiburg, Germany, "Likelihood-based observability analysis and confidence intervals for predictions of dynamic models"

10.30-11.00 Coffee break

11.00-11.30 David Gomez-Cabrero*, Stockholm, Sweden, "Workflow for generating competing hypothesis from models with parameter uncertainty"
11.30-12.00 Dennis Rickert*, (Nicolai Fricker, Inna Lavrik, Fabian J. Theis), Munich, Germany, "Set-based reduction of a CD95 signaling model of apoptosis allows new interpretation of existing data and design of new experimental strategies" (abstract)

Lunch 12-13.15

13.15-14.30 Group discussions
14.30-15.00 Coffee break

Session on Statistical and probabilistic approaches
15.00-15.30 Joep Vanlier*, Eindhoven, The Netherlands, "A Bayesian Approach to Predictions Despite Uncertainties"
15.30-16.00 Andrei Kramer*, Stuttgart, TBA (Bayesian approaches to parameter uncertainties)
16.00-17.00 Coffee break, final discussions on this session

19.00 Joint dinner downtown Linköping (restaurant Kniv och Gaffel)

Sunday June 19

Session on analytical, interval analysis, and set-based approaches

9.30-10.00 Jan Hasenauer*, Stuttgart, Germany, "Parameter identification, experimental design and model falsification for biological network models using semidefinite programming" (see IET Syst Biol. 2010, 4(2):119-30)
10.00-10.30 Pelle Lundberg* and Torkel Glad*, Linköping, Sweden, "Evaluation of BioSDP on realistic examples; accounting for the discretization error"
10.30-11.00 Discussion on the set-based approaches
11.00-11.30 Coffee break

11.30-12.00 Michel Kieffer*, Paris, France, "Applied Interval Analysis". Paper.
12.00-13.00 General discussion, future plans


* = confirmed


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