Model-Checking an Ecosystem Model for Decision-Aid

International audience—This work stems on the idea that timed automata models and model-checking techniques may bring much in a decision-aid context when dealing with large and interacting qualitative models. In this paper, we focus on two key issues when facing the interpretation and explanation of behavior in real-world systems: the model building and its exploration using logic patterns. We illustrate this approach in the ecological domain with the modeling and exploration of a fisheries ecosystem

Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)

In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect the imposed level of approximation provided that with increasing parameter value the approximation converges to the original continuous system. By employing this approximation technique, we present algorithms solving the reachability problem for biochemical dynamical systems. The presented method and algorithms are evaluated on several exemplary biological models and on a real case study.Comment: In Proceedings CompMod 2011, arXiv:1109.104

An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

Model checking is a well-established technique for automaticallyverifying complex systems. Recently, model checkers have appearedin computer tools for the analysis of biochemical (and generegulatory) networks. We survey several such tools to assess thepotential of model checking in computational biology. Next, our overviewfocuses on direct applications of existing model checkers, as well ason algorithms for biochemical network analysis influenced by modelchecking, such as those using binary decision diagrams or Booleansatisfiability solvers. We conclude with advantages and drawbacks ofmodel checking for the analysis of biochemical networks

Simulation product fidelity: a qualitative & quantitative system engineering approach

La modélisation informatique et la simulation sont des activités de plus en plus répandues lors de la conception de systèmes complexes et critiques tels que ceux embarqués dans les avions. Une proposition pour la conception et réalisation d'abstractions compatibles avec les objectifs de simulation est présentée basés sur la théorie de l'informatique, le contrôle et le système des concepts d'ingénierie. Il adresse deux problèmes fondamentaux de fidélité dans la simulation, c'est-à-dire, pour une spécification du système et quelques propriétés d'intérêt, comment extraire des abstractions pour définir une architecture de produit de simulation et jusqu'où quel point le comportement du modèle de simulation représente la spécification du système. Une notion générale de cette fidélité de la simulation, tant architecturale et comportementale, est expliquée dans les notions du cadre expérimental et discuté dans le contexte des abstractions de modélisation et des relations d'inclusion. Une approche semi-formelle basée sur l'ontologie pour construire et définir l'architecture de produit de simulation est proposée et démontrée sur une étude d'échelle industrielle. Une approche formelle basée sur le jeu théorique et méthode formelle est proposée pour différentes classes de modèles des systèmes et des simulations avec un développement d'outils de prototype et cas des études. Les problèmes dans la recherche et implémentation de ce cadre de fidélité sont discutées particulièrement dans un contexte industriel.In using Modeling and Simulation for the system Verification & Validation activities, often the difficulty is finding and implementing consistent abstractions to model the system being simulated with respect to the simulation requirements. A proposition for the unified design and implementation of modeling abstractions consistent with the simulation objectives based on the computer science, control and system engineering concepts is presented. It addresses two fundamental problems of fidelity in simulation, namely, for a given system specification and some properties of interest, how to extract modeling abstractions to define a simulation product architecture and how far does the behaviour of the simulation model represents the system specification. A general notion of this simulation fidelity, both architectural and behavioural, in system verification and validation is explained in the established notions of the experimental frame and discussed in the context of modeling abstractions and inclusion relations. A semi-formal ontology based domain model approach to build and define the simulation product architecture is proposed with a real industrial scale study. A formal approach based on game theoretic quantitative system refinement notions is proposed for different class of system and simulation models with a prototype tool development and case studies. Challenges in research and implementation of this formal and semi-formal fidelity framework especially in an industrial context are discussed

Timed model-based programming : executable specifications for robust mission-critical sequences

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2003.Includes bibliographical references (p. 195-204).There is growing demand for high-reliability embedded systems that operate robustly and autonomously in the presence of tight real-time constraints. For robotic spacecraft, robust plan execution is essential during time-critical mission sequences, due to the very short time available for recovery from anomalies. Traditional approaches to encoding these sequences can lead to brittle behavior under off-nominal execution conditions, due to the high level of complexity in the control specification required to manage the complex spacecraft system interactions. This work describes timed model-based programming, a novel approach for encoding and robustly executing mission-critical spacecraft sequences. The timed model-based programming approach addresses the issues of sequence complexity and unanticipated low-level system interactions by allowing control programs to directly read or write "hidden" states of the plant, that is, states that are not directly observable or controllable. It is then the responsibility of the program's execution kernel to map between hidden states and the plant sensors and control variables. This mapping is performed automatically by a deductive controller using a common-sense plant model, freeing the programmer from the error-prone process of reasoning through a complex set of interactions under a range of possible failure situations. Time is central to the execution of mission-critical sequences; a robust executive must consider time in its control and behavior models, in addition to reactively managing complexity.(cont.) In timed model-based programming, control programs express goals and constraints in terms of both system state and time. Plant models capture the underlying behavior of the system components, including nominal and off-nominal modes, probabilistic transitions, and timed effects such as state transition latency. The contributions of this work are threefold. First, a semantic specification of the timed model-based programming approach is provided. The execution semantics of a timed model-based program are defined in terms of legal state evolutions of a physical plant, represented as a factored Partially Observable Semi-Markov Decision Process. The second contribution is the definition of graphical and textual languages for encoding timed control programs and plant models. The adoption of a visual programming paradigm allows timed model-based programs to be specified and readily inspected by the systems engineers in charge of designing the mission-critical sequences. The third contribution is the development of a Timed Model-based Executive, which takes as input a timed control program and executes it, using timed plant models to track states, diagnose faults and generate control actions. The Timed Model-based Executive has been implemented and demonstrated on a representative spacecraft scenario for Mars entry, descent and landing.by Michel Donald Ingham.Sc.D

Model building and model checking for biochemical processes

A central claim of computational systems biology is that, by drawing on mathematical approaches developed in the context of dynamic systems, kinetic analysis, computational theory and logic, it is possible to create powerful simulation, analysis, and reasoning tools for working biologists to decipher existing data, devise new experiments, and ultimately to understand functional properties of genomes, proteomes, cells, organs, and organisms. In this article, a novel computational tool is described that achieves many of the goals of this new discipline. The novelty of this system involves an automaton-based semantics of the temporal evolution of complex biochemical reactions starting from the representation given as a set of differential equations. The related tools also provide ability to qualitatively reason about the systems using a propositional temporal logic that can express an ordered sequence of events succinctly and unambiguously. The implementation of mathematical and computational models in the Simpathica and XSSYS systems is described briefly. Several example applications of these systems to cellular and biochemical processes are presented: the two most prominent are Leibler et al.'s repressilator (an artificial synthesized oscillatory network), and Curto-Voit-Sorribas-Cascante's purine metabolism reaction model

Self-Stabilizing Message Routing in Mobile ad hoc Networks

We present a self-stabilizing algorithm for routing messages between arbitrary pairs of nodes in a mobile ad hoc network. Our algorithm assumes the availability of a reliable GPS service, which supplies mobile nodes with accurate information about real time and about their own geographical locations. The GPS service provides an external, shared source of consistency for mobile nodes, allowing them to label and timestamp messages, and thereby aiding in recovery from failures. Our algorithm utilizes a Virtual Infrastructure programming abstraction layer, consisting of mobile client nodes, virtual stationary timed machines called Virtual Stationary Automata (VSAs), and a local broadcast service connecting VSAs and mobile clients. VSAs are associated with predetermined regions in the plane, and are emulated in a self-stabilizing manner by the mobile nodes. VSAs are relatively stable in the face of node mobility and failure, and can be used to simplify algorithm development for mobile networks. Our routing algorithm consists of three subalgorithms: [(1)] a VSA-to-VSA geographical routing algorithm, [2] a mobile client location management algorithm, and [3] the main algorithm, which utilizes both location management and geographical routing. All three subalgorithms are self-stabilizing, and consequently, the entire algorithm is also self-stabilizing

Timing Robustness in the Budding and Fission Yeast Cell Cycles

Robustness of biological models has emerged as an important principle in systems biology. Many past analyses of Boolean models update all pending changes in signals simultaneously (i.e., synchronously), making it impossible to consider robustness to variations in timing that result from noise and different environmental conditions. We checked previously published mathematical models of the cell cycles of budding and fission yeast for robustness to timing variations by constructing Boolean models and analyzing them using model-checking software for the property of speed independence. Surprisingly, the models are nearly, but not totally, speed-independent. In some cases, examination of timing problems discovered in the analysis exposes apparent inaccuracies in the model. Biologically justified revisions to the model eliminate the timing problems. Furthermore, in silico random mutations in the regulatory interactions of a speed-independent Boolean model are shown to be unlikely to preserve speed independence, even in models that are otherwise functional, providing evidence for selection pressure to maintain timing robustness. Multiple cell cycle models exhibit strong robustness to timing variation, apparently due to evolutionary pressure. Thus, timing robustness can be a basis for generating testable hypotheses and can focus attention on aspects of a model that may need refinement