Modelling and Analysis Using GROOVE

In this paper we present case studies that describe how the graph transformation tool GROOVE has been used to model problems from a wide variety of domains. These case studies highlight the wide applicability of GROOVE in particular, and of graph transformation in general. They also give concrete templates for using GROOVE in practice. Furthermore, we use the case studies to analyse the main strong and weak points of GROOVE

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Towards Translating Graph Transformation Approaches by Model Transformations

Recently, many researchers are working on semantics preserving model transformation. In the field of graph transformation one can think of translating graph grammars written in one approach to a behaviourally equivalent graph grammar in another approach. In this paper we translate graph grammars developed with the GROOVE tool to AGG graph grammars by first investigating the set of core graph transformation concepts supported by both tools. Then, we define what it means for two graph grammars to be behaviourally equivalent, and for the regarded approaches we actually show how to handle different definitions of both - application conditions and graph structures. The translation itself is explained by means of intuitive examples

Ontology-based patterns for the integration of business processes and enterprise application architectures

Increasingly, enterprises are using Service-Oriented Architecture (SOA) as an approach to Enterprise Application Integration (EAI). SOA has the potential to bridge the gap between business and technology and to improve the reuse of existing applications and the interoperability with new ones. In addition to service architecture descriptions, architecture abstractions like patterns and styles capture design knowledge and allow the reuse of successfully applied designs, thus improving the quality of software. Knowledge gained from integration projects can be captured to build a repository of semantically enriched, experience-based solutions. Business patterns identify the interaction and structure between users, business processes, and data. Specific integration and composition patterns at a more technical level address enterprise application integration and capture reliable architecture solutions. We use an ontology-based approach to capture architecture and process patterns. Ontology techniques for pattern definition, extension and composition are developed and their applicability in business process-driven application integration is demonstrated