ETAPS 2019
Sat 6 - Thu 11 April 2019 Prague, Czech Republic
Sun 7 Apr 2019 16:30 - 17:00 at S9 - Synthesis and Inference Chair(s): Michela Chiappalone

Symbolic systems biology aims to explore biological processes as whole systems instead of small and independent elements. The goal is to define formal models that capture biologists intuitions and reasoning. Pathway Logic is a system for developing executable formal models of biomolecular processes. Using the Maude system, these models of dynamic processes can be represented and analyzed. The Pathway Logic Assistant uses forwards and backwards collection to assemble a connected set of rules from a rule knowledge base to model a system specified by an initial state (experimental setup). For this to succeed the rules must represent component states at the same level of detail, while we would like the knowledge base to capture as much detail as possible. In this paper, we propose a different way to perform matching in the process of rewriting in the high-performance rewriting language Maude. The basic concept is that of ‘‘fuzzy match’’ or ‘‘fuzzy instantiates to’’. It will be used to check requirements imposed by controls in forward collection, and with some elaboration to check whether the change part of a rule applies forwards or backwards.

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