3,315 research outputs found

    Types for BioAmbients

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    The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each ambient with group types specifying the kind of compartments in which the ambient can stay. The type system ensures that, in a well-typed process, ambients cannot be nested in a way that violates the type hierarchy. Exploiting the information given by the group types, we also extend the operational semantics of BioAmbients with rules signalling errors that may derive from undesired ambients' moves (i.e. merging incompatible tissues). Thus, the signal of errors can help the modeller to detect and locate unwanted situations that may arise in a biological system, and give practical hints on how to avoid the undesired behaviour

    Adaptability Checking in Multi-Level Complex Systems

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    A hierarchical model for multi-level adaptive systems is built on two basic levels: a lower behavioural level B accounting for the actual behaviour of the system and an upper structural level S describing the adaptation dynamics of the system. The behavioural level is modelled as a state machine and the structural level as a higher-order system whose states have associated logical formulas (constraints) over observables of the behavioural level. S is used to capture the global and stable features of B, by a defining set of allowed behaviours. The adaptation semantics is such that the upper S level imposes constraints on the lower B level, which has to adapt whenever it no longer can satisfy them. In this context, we introduce weak and strong adaptabil- ity, i.e. the ability of a system to adapt for some evolution paths or for all possible evolutions, respectively. We provide a relational characterisation for these two notions and we show that adaptability checking, i.e. deciding if a system is weak or strong adaptable, can be reduced to a CTL model checking problem. We apply the model and the theoretical results to the case study of motion control of autonomous transport vehicles.Comment: 57 page, 10 figures, research papaer, submitte

    Programmable models of growth and mutation of cancer-cell populations

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    In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

    Stochastic Calculus of Wrapped Compartments

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    The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the patterns to be matched in a term (whose complexity in CLS is strongly affected by the variables matching in the sequences). We define a stochastic semantics for this new calculus. As an application we model the interaction between macrophages and apoptotic neutrophils and a mechanism of gene regulation in E.Coli

    Towards Theory of Massive-Parallel Proofs. Cellular Automata Approach

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    In the paper I sketch a theory of massively parallel proofs using cellular automata presentation of deduction. In this presentation inference rules play the role of cellular-automatic local transition functions. In this approach we completely avoid axioms as necessary notion of deduction theory and therefore we can use cyclic proofs without additional problems. As a result, a theory of massive-parallel proofs within unconventional computing is proposed for the first time.Comment: 13 page

    A Language-centered Approach to support environmental modeling with Cellular Automata

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    Die Anwendung von Methodiken und Technologien aus dem Bereich der Softwaretechnik auf den Bereich der Umweltmodellierung ist eine gemeinhin akzeptierte Vorgehensweise. Im Rahmen der "modellgetriebenen Entwicklung"(MDE, model-driven engineering) werden Technologien entwickelt, die darauf abzielen, Softwaresysteme vorwiegend auf Basis von im Vergleich zu Programmquelltexten relativ abstrakten Modellen zu entwickeln. Ein wesentlicher Bestandteil von MDE sind Techniken zur effizienten Entwicklung von "domänenspezifischen Sprachen"( DSL, domain-specific language), die auf Sprachmetamodellen beruhen. Die vorliegende Arbeit zeigt, wie modellgetriebene Entwicklung, und insbesondere die metamodellbasierte Beschreibung von DSLs, darüber hinaus Aspekte der Pragmatik unterstützen kann, deren Relevanz im erkenntnistheoretischen und kognitiven Hintergrund wissenschaftlichen Forschens begründet wird. Hierzu wird vor dem Hintergrund der Erkenntnisse des "modellbasierten Forschens"(model-based science und model-based reasoning) gezeigt, wie insbesondere durch Metamodelle beschriebene DSLs Möglichkeiten bieten, entsprechende pragmatische Aspekte besonders zu berücksichtigen, indem sie als Werkzeug zur Erkenntnisgewinnung aufgefasst werden. Dies ist v.a. im Kontext großer Unsicherheiten, wie sie für weite Teile der Umweltmodellierung charakterisierend sind, von grundsätzlicher Bedeutung. Die Formulierung eines sprachzentrierten Ansatzes (LCA, language-centered approach) für die Werkzeugunterstützung konkretisiert die genannten Aspekte und bildet die Basis für eine beispielhafte Implementierung eines Werkzeuges mit einer DSL für die Beschreibung von Zellulären Automaten (ZA) für die Umweltmodellierung. Anwendungsfälle belegen die Verwendbarkeit von ECAL und der entsprechenden metamodellbasierten Werkzeugimplementierung.The application of methods and technologies of software engineering to environmental modeling and simulation (EMS) is common, since both areas share basic issues of software development and digital simulation. Recent developments within the context of "Model-driven Engineering" (MDE) aim at supporting the development of software systems at the base of relatively abstract models as opposed to programming language code. A basic ingredient of MDE is the development of methods that allow the efficient development of "domain-specific languages" (DSL), in particular at the base of language metamodels. This thesis shows how MDE and language metamodeling in particular, may support pragmatic aspects that reflect epistemic and cognitive aspects of scientific investigations. For this, DSLs and language metamodeling in particular are set into the context of "model-based science" and "model-based reasoning". It is shown that the specific properties of metamodel-based DSLs may be used to support those properties, in particular transparency, which are of particular relevance against the background of uncertainty, that is a characterizing property of EMS. The findings are the base for the formulation of an corresponding specific metamodel- based approach for the provision of modeling tools for EMS (Language-centered Approach, LCA), which has been implemented (modeling tool ECA-EMS), including a new DSL for CA modeling for EMS (ECAL). At the base of this implementation, the applicability of this approach is shown

    Model Checking Markov Chains with Actions and State Labels

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    In the past, logics of several kinds have been proposed for reasoning about discrete- or continuous-time Markov chains. Most of these logics rely on either state labels (atomic propositions) or on transition labels (actions). However, in several applications it is useful to reason about both state-properties and action-sequences. For this purpose, we introduce the logic asCSL which provides powerful means to characterize execution paths of Markov chains with actions and state labels. asCSL can be regarded as an extension of the purely state-based logic asCSL (continuous stochastic logic). \ud In asCSL, path properties are characterized by regular expressions over actions and state-formulas. Thus, the truth value of path-formulas does not only depend on the available actions in a given time interval, but also on the validity of certain state formulas in intermediate states.\ud We compare the expressive power of CSL and asCSL and show that even the state-based fragment of asCSL is strictly more expressive than CSL if time intervals starting at zero are employed. Using an automaton-based technique, an asCSL formula and a Markov chain with actions and state labels are combined into a product Markov chain. For time intervals starting at zero we establish a reduction of the model checking problem for asCSL to CSL model checking on this product Markov chain. The usefulness of our approach is illustrated by through an elaborate model of a scalable cellular communication system for which several properties are formalized by means of asCSL-formulas, and checked using the new procedure
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