AG 1, AG 2, AG 3, AG 4, AG 5, SWS, RG1, MMCI   Info

Public Audience

English

60 Minutes

Saarbrücken

Symbolic Methods bear the promise to cope with the high parameter
uncertainty commonly found in biological networks. Using logical and
algebraic tools for satisfiability checking in the first-order theory of
the reals qualitative questions such as the ones asking for
multi-stationarity or existence of oscillations can be answered by
providing logical formulae describing the corresponding fulfilling
parameter regions. We provide a case study involving models of the MAPK
cascade, an important signalling pathway.
On the one hand the promise comes at the cost of high worst case
complexity of the symbolic methods (used in the case study). On the
other hand approximation techniques using ideas from Tropical Geometry
can be applied, which have a sound theoretic foundation and also deal
with parameter uncertainty. Identification of "slow" parameters, an
essential prerequisite for many model reduction techniques, and even
candidates for metastable regimes can be obtained by analyzing the
solution polytopes of certain Tropical Equilibration problems. Whereas
the Tropical Equilibration problem is NP-hard in its generic form,
computation results obtained on the BIOMOD database indicate that its
restriction to instances arising from biochemical networks might be
tractable.

Jennifer Müller

2900

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