BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Abstract Interpretation for Probabilistic Termination of Biological Systems

In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting the multiplicity of reagents present in a solution, using intervals. In this paper, we refine the approach in order to address probabilistic termination properties. More in details, we introduce a refinement of the abstract LTS semantics and we abstract the probabilistic semantics using a variant of Interval Markov Chains. The abstract probabilistic model safely approximates a set of concrete experiments and reports conservative lower and upper bounds for probabilistic termination

Analyse pire cas exact du réseau AFDX

L'objectif principal de cette thèse est de proposer les méthodes permettant d'obtenir le délai de transmission de bout en bout pire cas exact d'un réseau AFDX. Actuellement, seules des bornes supérieures pessimistes peuvent être calculées en utilisant les approches de type Calcul Réseau ou par Trajectoires. Pour cet objectif, différentes approches et outils existent et ont été analysées dans le contexte de cette thèse. Cette analyse a mis en évidence le besoin de nouvelles approches. Dans un premier temps, la vérification de modèle a été explorée. Les automates temporisés et les outils de verification ayant fait leur preuve dans le domaine temps réel ont été utilisés. Ensuite, une technique de simulation exhaustive a été utilisée pour obtenir les délais de communication pire cas exacts. Pour ce faire, des méthodes de réduction de séquences ont été définies et un outil a été développé. Ces méthodes ont été appliquées à une configuration réelle du réseau AFDX, nous permettant ainsi de valider notre travail sur une configuration de taille industrielle du réseau AFDX telle que celle embarquée à bord des avions Airbus A380. The main objective of this thesis is to provide methodologies for finding exact worst case end to end communication delays of AFDX network. Presently, only pessimistic upper bounds of these delays can be calculated by using Network Calculus and Trajectory approach. To achieve this goal, different existing tools and approaches have been analyzed in the context of this thesis. Based on this analysis, it is deemed necessary to develop new approaches and algorithms. First, Model checking with existing well established real time model checking tools are explored, using timed automata. Then, exhaustive simulation technique is used with newly developed algorithms and their software implementation in order to find exact worst case communication delays of AFDX network. All this research work has been applied on real life implementation of AFDX network, allowing us to validate our research work on industrial scale configuration of AFDX network such as used on Airbus A380 aircraft. ABSTRACT : The main objective of this thesis is to provide methodologies for finding exact worst case end to end communication delays of AFDX network. Presently, only pessimistic upper bounds of these delays can be calculated by using Network Calculus and Trajectory approach. To achieve this goal, different existing tools and approaches have been analyzed in the context of this thesis. Based on this analysis, it is deemed necessary to develop new approaches and algorithms. First, Model checking with existing well established real time model checking tools are explored, using timed automata. Then, exhaustive simulation technique is used with newly developed algorithms and their software implementation in order to find exact worst case communication delays of AFDX network. All this research work has been applied on real life implementation of AFDX network, allowing us to validate our research work on industrial scale configuration of AFDX network such as used on Airbus A380 aircraft

Algebraic Properties of Qualitative Spatio-Temporal Calculi

Qualitative spatial and temporal reasoning is based on so-called qualitative calculi. Algebraic properties of these calculi have several implications on reasoning algorithms. But what exactly is a qualitative calculus? And to which extent do the qualitative calculi proposed meet these demands? The literature provides various answers to the first question but only few facts about the second. In this paper we identify the minimal requirements to binary spatio-temporal calculi and we discuss the relevance of the according axioms for representation and reasoning. We also analyze existing qualitative calculi and provide a classification involving different notions of a relation algebra.Comment: COSIT 2013 paper including supplementary materia

Computational physics of the mind

In the XIX century and earlier such physicists as Newton, Mayer, Hooke, Helmholtz and Mach were actively engaged in the research on psychophysics, trying to relate psychological sensations to intensities of physical stimuli. Computational physics allows to simulate complex neural processes giving a chance to answer not only the original psychophysical questions but also to create models of mind. In this paper several approaches relevant to modeling of mind are outlined. Since direct modeling of the brain functions is rather limited due to the complexity of such models a number of approximations is introduced. The path from the brain, or computational neurosciences, to the mind, or cognitive sciences, is sketched, with emphasis on higher cognitive functions such as memory and consciousness. No fundamental problems in understanding of the mind seem to arise. From computational point of view realistic models require massively parallel architectures