Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA

This paper examines the influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway [5] through modelling in a Markovian process algebra, PEPA [11]. Two models of the system are presented, a reagent-centric view and a pathway-centric view. The models capture functionality at the level of subpathway, rather than at a molecular level. Each model affords a different perspective of the pathway and analysis. We demonstrate the two models to be formally equivalent using the timing-aware bisimulation defined over PEPA models and discuss the biological significance

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)

Colored Petri nets in the simulation of ETL standard tasks: the surrogate key pipelining case

ETL (Extract-Transform-Load) systems are formed by processes responsible for the extraction of data from several sources, cleaning and transforming it in accordance with some prerequisites of a data warehouse, and finally loading it in its multidimensional structures. ETL processes are the most complex tasks involved within the development of a Data Warehousing System, being crucial to model them previously so that, during the implementation stage, the correct set of requirements is considered. Coloured Petri Nets are a graphical modelling language used in the design, specification, simulation and validation of large systems, characterized as being strongly concurrent. The objective of this manuscript is to discuss the application of Coloured Petri Nets to the specification and validation of ETL systems. To demonstrate their viability for such tasks we have selected one of the most relevant and used case in ETL systems implementation: a surrogate key pipelining

Abridged Petri Nets

A new graphical framework, Abridged Petri Nets (APNs) is introduced for bottom-up modeling of complex stochastic systems. APNs are similar to Stochastic Petri Nets (SPNs) in as much as they both rely on component-based representation of system state space, in contrast to Markov chains that explicitly model the states of an entire system. In both frameworks, so-called tokens (denoted as small circles) represent individual entities comprising the system; however, SPN graphs contain two distinct types of nodes (called places and transitions) with transitions serving the purpose of routing tokens among places. As a result, a pair of place nodes in SPNs can be linked to each other only via a transient stop, a transition node. In contrast, APN graphs link place nodes directly by arcs (transitions), similar to state space diagrams for Markov chains, and separate transition nodes are not needed. Tokens in APN are distinct and have labels that can assume both discrete values ("colors") and continuous values ("ages"), both of which can change during simulation. Component interactions are modeled in APNs using triggers, which are either inhibitors or enablers (the inhibitors' opposites). Hierarchical construction of APNs rely on using stacks (layers) of submodels with automatically matching color policies. As a result, APNs provide at least the same modeling power as SPNs, but, as demonstrated by means of several examples, the resulting models are often more compact and transparent, therefore facilitating more efficient performance evaluation of complex systems.Comment: 17 figure

Analysing Coloured Petri Nets by the Occurrence Graph Method

This paper provides an overview og the work done for the author's PhD thesis. The research area of Coloured Petri Nets is introduced, and the available analysis methods are presented. The occurrence graph method, which is the main subject of this thesis, is described in more detail. Summaries of the six papers which, together with this overview, comprise the thesis are given, and the contributions are discussed.A large portion of this overview is dedicated to a description of related work. The aim is twofold: First, to survey pertinent results within the research areas of -- in increasing generality -- Coloured Petri Nets, High-level Petri Nets, and formalisms for modelling and analysis of parallel and distributed systems. Second, to put the results obtained in this thesis in a wider perspective by comparing them with important related work