Setting Parameters for Biological Models With ANIMO

ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entities in form of a graph, while the parameters determine the speed of occurrence of such interactions. When a mismatch is observed between the behavior of an ANIMO model and experimental data, we want to update the model so that it explains the new data. In general, the topology of a model can be expanded with new (known or hypothetical) nodes, and enables it to match experimental data. However, the unrestrained addition of new parts to a model causes two problems: models can become too complex too fast, to the point of being intractable, and too many parts marked as "hypothetical" or "not known" make a model unrealistic. Even if changing the topology is normally the easier task, these problems push us to try a better parameter fit as a first step, and resort to modifying the model topology only as a last resource. In this paper we show the support added in ANIMO to ease the task of expanding the knowledge on biological networks, concentrating in particular on the parameter settings

Re-verification of a Lip Synchronization Algorithm using robust reachability

The timed automata formalism is an important model for specifying and analysing real-time systems. Robustness is the correctness of the model in the presence of small drifts on clocks or imprecision in testing guards. A symbolic algorithm for the analysis of the robustness of timed automata has been implemented. In this paper we re-analyse an industrial case lip synchronization protocol using the new robust reachability algorithm.This lip synchronization protocol is an interesting case because timing aspect are crucial for the correctness of the protocol. Several versions of the model are considered, with an ideal video stream, with anchored jitter, and with non-anchored jitter

Re-verification of a Lip Synchronization Protocol using Robust Reachability

The timed automata formalism is an important model for specifying and analysing real-time systems. Robustness is the correctness of the model in the presence of small drifts on clocks or imprecision in testing guards. A symbolic algorithm for the analysis of the robustness of timed automata has been implemented. In this paper, we re-analyse an industrial case lip synchronization protocol using the new robust reachability algorithm. This lip synchronization protocol is an interesting case because timing aspects are crucial for the correctness of the protocol. Several versions of the model are considered: with an ideal video stream, with anchored jitter, and with non-anchored jitter

Quantitative testing

We investigate the problem of specification based testing with dense sets of inputs and outputs, in particular with imprecision as they might occur due to errors in measurements, numerical instability or noisy channels. Using quantitative transition systems to describe implementations and specifications, we introduce implementation relations that capture a notion of correctness “up to ε”, allowing deviations of implementation from the specification of at most ε. These quantitative implementation relations are described as Hausdorff distances between certain sets of traces. They are conservative extensions of the well-known ioco relation. We develop an on-line and an off-line algorithm to generate test cases from a requirement specification, modeled as a quantitative transition system. Both algorithms are shown to be sound and complete with respect to the quantitative implementation relations introduced

Robust Analysis of Timed Automata via Channel Machines

International audienceWhereas formal verification of timed systems has become a very active field of research, the idealised mathematical semantics of timed automata cannot be faithfully implemented. Several works have thus focused on a modified semantics of timed automata which ensures implementability, and robust model-checking algorithms for safety, and later LTL properties have been designed. Recently, a~new approach has been proposed, which reduces (standard) model-checking of timed automata to other verification problems on channel machines. Thanks to a new encoding of the modified semantics as a network of timed systems, we propose an original combination of both approaches, and prove that robust model-checking for coFlat-MTL, a large fragment of~MTL, is EXPSPACE-Complete

Quantitative Robustness Analysis of Flat Timed Automata

Whereas formal verification of timed systems has become a very active field of research, the idealized mathematical semantics of timed automata cannot be faithfully implemented. Recently, several works have studied a parametric semantics of timed automata related to implementability: if the specification is met for some positive value of the parameter, then there exists a correct implementation. In addition, the value of the parameter gives lower bounds on sufficient resources for the implementation. In this work, we present a symbolic algorithm for the computation of the parametric reachability set under this semantics for flat timed automata. As a consequence, we can compute the largest value of the parameter for a timed automaton to be safe

Robust safety of timed automata

Timed automata are governed by an idealized semantics that assumes a perfectly precise behavior of the clocks. The traditional semantics is not robust because the slightest perturbation in the timing of actions may lead to completely different behaviors of the automaton. Following several recent works, we consider a relaxation of this semantics, in which guards on transitions are widened byΔ>0 and clocks can drift byε>0. The relaxed semantics encompasses the imprecisions that are inevitably present in an implementation of a timed automaton, due to the finite precision of digital clocks. We solve the safety verification problem for this robust semantics: given a timed automaton and a set of bad states, our algorithm decides if there exist positive values for the parametersΔ andε such that the timed automaton never enters the bad states under the relaxed semantic

Self-Evaluation Applied Mathematics 2003-2008 University of Twente

This report contains the self-study for the research assessment of the Department of Applied Mathematics (AM) of the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) at the University of Twente (UT). The report provides the information for the Research Assessment Committee for Applied Mathematics, dealing with mathematical sciences at the three universities of technology in the Netherlands. It describes the state of affairs pertaining to the period 1 January 2003 to 31 December 2008