Building Confidence in Quantitative Systems Pharmacology Models : An Engineer's Guide to Exploring the Rationale in Model Design and Development

This tutorial promotes good practice for exploring the rationale of systems pharmacology models. A safety systems engineering inspired notation approach provides much needed rigor and transparency in development and application of models for therapeutic discovery and design of intervention strategies. Structured arguments over a model's development, underpinning biological knowledge, and analyses of model behaviors are constructed to determine the confidence that a model is fit for the purpose for which it will be applied

Automating the transformation-based analysis of visual languages

The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-009-0114-yWe present a novel approach for the automatic generation of model-to-model transformations given a description of the operational semantics of the source language in the form of graph transformation rules. The approach is geared to the generation of transformations from Domain-Specific Visual Languages (DSVLs) into semantic domains with an explicit notion of transition, like for example Petri nets. The generated transformation is expressed in the form of operational triple graph grammar rules that transform the static information (initial model) and the dynamics (source rules and their execution control structure). We illustrate these techniques with a DSVL in the domain of production systems, for which we generate a transformation into Petri nets. We also tackle the description of timing aspects in graph transformation rules, and its analysis through their automatic translation into Time Petri netsWork sponsored by the Spanish Ministry of Science and Innovation, project METEORIC (TIN2008-02081/TIN) and by the Canadian Natural Sciences and Engineering Research Council (NSERC)

Scale-invariant cellular automata and self-similar Petri nets

Two novel computing models based on an infinite tessellation of space-time are introduced. They consist of recursively coupled primitive building blocks. The first model is a scale-invariant generalization of cellular automata, whereas the second one utilizes self-similar Petri nets. Both models are capable of hypercomputations and can, for instance, "solve" the halting problem for Turing machines. These two models are closely related, as they exhibit a step-by-step equivalence for finite computations. On the other hand, they differ greatly for computations that involve an infinite number of building blocks: the first one shows indeterministic behavior whereas the second one halts. Both models are capable of challenging our understanding of computability, causality, and space-time.Comment: 35 pages, 5 figure

Representing Conversations for Scalable Overhearing

Open distributed multi-agent systems are gaining interest in the academic community and in industry. In such open settings, agents are often coordinated using standardized agent conversation protocols. The representation of such protocols (for analysis, validation, monitoring, etc) is an important aspect of multi-agent applications. Recently, Petri nets have been shown to be an interesting approach to such representation, and radically different approaches using Petri nets have been proposed. However, their relative strengths and weaknesses have not been examined. Moreover, their scalability and suitability for different tasks have not been addressed. This paper addresses both these challenges. First, we analyze existing Petri net representations in terms of their scalability and appropriateness for overhearing, an important task in monitoring open multi-agent systems. Then, building on the insights gained, we introduce a novel representation using Colored Petri nets that explicitly represent legal joint conversation states and messages. This representation approach offers significant improvements in scalability and is particularly suitable for overhearing. Furthermore, we show that this new representation offers a comprehensive coverage of all conversation features of FIPA conversation standards. We also present a procedure for transforming AUML conversation protocol diagrams (a standard human-readable representation), to our Colored Petri net representation

08361 Abstracts Collection -- Programming Multi-Agent Systems

From 31th August to 5th September, the Dagstuhl Seminar 08361 ``Programming Multi-Agent Systems\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Civilising Globalism: Transnational Norm-Building Networks—A Research Programme

Decentralised, self-organised cross-border activities are increasingly shaping global policymaking. While state actors have lost ground, policy and economic networks have emerged as key actors, transforming international relations as well as national spheres. Academic discourse is following their activity, often focusing on "advocacy networks" and on the role of transnational actors within the transformation of the world economy and world polity. In contrast to these research activities, the approach proposed here extends the scope of inquiry to include the role of transnational networks in norm-building and norm-implementation. The networks under scrutiny here do not confine themselves to the articulation of particular interests, the resolution of particular conflicts, or compliance with legal norms. It is presumed here that a variety of networks which are fundamentally concerned with the creation of norms have emerged. The predominance of the nation-state, one of the main characteristics of modern democratic thinking, has eroded to the point where the fundamental nexus of voice (democratic participation) and entitlement (legal and social rights and duties) has been weakened or even broken. We presume that this decentration has fundamentally changed the option of voice as one of the most important responses by citizens to crisis and change. This comes to the fore with the emergence and effectiveness of transnational norm-building networks. The article develops a research programme, the outcome of which will shed light on this new resource for the development of a democratised world polity.networks, norms, world polity, globalisation, global civil society

Decision systems : the relation between problem specification and mathematical analysis

In this paper it is demonstrated that automated support for decision making of a tactical or strategic nature requires a solver-independent medium for describing decision situations. Such a medium may be specific for one environment, but it is also possible to develop media for certain types of environments. By using such a medium one obtains a decoupling of problem formulation and method of analysis. This makes it possible to use (parts of) the problem formulation as input for different types of models. Such problem formulations may provide mathematical models themselves, although they might also contain some less formal features. The decoupling makes it possible to choose problem formulations which are much closer to the original decision situation than would otherwise be possible with formulations in terms of a preselected solver. The argumentation is illustrated by treating a language for specifying goods flow problems in some detail. This language is based on timed coloured Petri-nets