Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

On Modelling and Analysis of Dynamic Reconfiguration of Dependable Real-Time Systems

This paper motivates the need for a formalism for the modelling and analysis of dynamic reconfiguration of dependable real-time systems. We present requirements that the formalism must meet, and use these to evaluate well established formalisms and two process algebras that we have been developing, namely, Webpi and CCSdp. A simple case study is developed to illustrate the modelling power of these two formalisms. The paper shows how Webpi and CCSdp represent a significant step forward in modelling adaptive and dependable real-time systems.Comment: Presented and published at DEPEND 201

Modelling Requirements for Content Recommendation Systems

This paper addresses the modelling of requirements for a content Recommendation System (RS) for Online Social Networks (OSNs). On OSNs, a user switches roles constantly between content generator and content receiver. The goals and softgoals are different when the user is generating a post, as opposed as replying to a post. In other words, the user is generating instances of different entities, depending on the role she has: a generator generates instances of a "post", while the receiver generates instances of a "reply". Therefore, we believe that when addressing Requirements Engineering (RE) for RS, it is necessary to distinguish these roles clearly. We aim to model an essential dynamic on OSN, namely that when a user creates (posts) content, other users can ignore that content, or themselves start generating new content in reply, or react to the initial posting. This dynamic is key to designing OSNs, because it influences how active users are, and how attractive the OSN is for existing, and to new users. We apply a well-known Goal Oriented RE (GORE) technique, namely i-star, and show that this language fails to capture this dynamic, and thus cannot be used alone to model the problem domain. Hence, in order to represent this dynamic, its relationships to other OSNs' requirements, and to capture all relevant information, we suggest using another modelling language, namely Petri Nets, on top of i-star for the modelling of the problem domain. We use Petri Nets because it is a tool that is used to simulate the dynamic and concurrent activities of a system and can be used by both practitioners and theoreticians.Comment: 28 pages, 7 figure

Subtyping for Hierarchical, Reconfigurable Petri Nets

Hierarchical Petri nets allow a more abstract view and reconfigurable Petri nets model dynamic structural adaptation. In this contribution we present the combination of reconfigurable Petri nets and hierarchical Petri nets yielding hierarchical structure for reconfigurable Petri nets. Hierarchies are established by substituting transitions by subnets. These subnets are themselves reconfigurable, so they are supplied with their own set of rules. Moreover, global rules that can be applied in all of the net, are provided

Integration of an object formalism within a hybrid dynamic simulation environment

PrODHyS is a general object-oriented environment which provides common and reusable components designed for the development and the management of dynamic simulation of systems engineering. Its major characteristic is its ability to simulate processes described by a hybrid model. In this framework, this paper focuses on the "Object Differential Petri Net" (ODPN) formalism integrated within PrODHyS. The use of this formalism is illustrated through a didactic example relating to the field of Chemical Process System Engineering (PSE)

Test of preemptive real-time systems

Time Petri nets with stopwatches not only model system/environment interactions and time constraints. They further enable modeling of suspend/resume operations in real-time systems. Assuming the modelled systems are non deterministic and partially observable, the paper proposes a test generation approach which implements an online testing policy and outputs test results that are valid for the (part of the) selected environment. A relativized conformance relation named rswtioco is defined and a test generation algorithm is presented. The proposed approach is illustrated on an example

A Process Modelling Framework Based on Point Interval Temporal Logic with an Application to Modelling Patient Flows

This thesis considers an application of a temporal theory to describe and model the patient journey in the hospital accident and emergency (A&E) department. The aim is to introduce a generic but dynamic method applied to any setting, including healthcare. Constructing a consistent process model can be instrumental in streamlining healthcare issues. Current process modelling techniques used in healthcare such as flowcharts, unified modelling language activity diagram (UML AD), and business process modelling notation (BPMN) are intuitive and imprecise. They cannot fully capture the complexities of the types of activities and the full extent of temporal constraints to an extent where one could reason about the flows. Formal approaches such as Petri have also been reviewed to investigate their applicability to the healthcare domain to model processes. Additionally, to schedule patient flows, current modelling standards do not offer any formal mechanism, so healthcare relies on critical path method (CPM) and program evaluation review technique (PERT), that also have limitations, i.e. finish-start barrier. It is imperative to specify the temporal constraints between the start and/or end of a process, e.g., the beginning of a process A precedes the start (or end) of a process B. However, these approaches failed to provide us with a mechanism for handling these temporal situations. If provided, a formal representation can assist in effective knowledge representation and quality enhancement concerning a process. Also, it would help in uncovering complexities of a system and assist in modelling it in a consistent way which is not possible with the existing modelling techniques. The above issues are addressed in this thesis by proposing a framework that would provide a knowledge base to model patient flows for accurate representation based on point interval temporal logic (PITL) that treats point and interval as primitives. These objects would constitute the knowledge base for the formal description of a system. With the aid of the inference mechanism of the temporal theory presented here, exhaustive temporal constraints derived from the proposed axiomatic system’ components serves as a knowledge base. The proposed methodological framework would adopt a model-theoretic approach in which a theory is developed and considered as a model while the corresponding instance is considered as its application. Using this approach would assist in identifying core components of the system and their precise operation representing a real-life domain deemed suitable to the process modelling issues specified in this thesis. Thus, I have evaluated the modelling standards for their most-used terminologies and constructs to identify their key components. It will also assist in the generalisation of the critical terms (of process modelling standards) based on their ontology. A set of generalised terms proposed would serve as an enumeration of the theory and subsume the core modelling elements of the process modelling standards. The catalogue presents a knowledge base for the business and healthcare domains, and its components are formally defined (semantics). Furthermore, a resolution theorem-proof is used to show the structural features of the theory (model) to establish it is sound and complete. After establishing that the theory is sound and complete, the next step is to provide the instantiation of the theory. This is achieved by mapping the core components of the theory to their corresponding instances. Additionally, a formal graphical tool termed as point graph (PG) is used to visualise the cases of the proposed axiomatic system. PG facilitates in modelling, and scheduling patient flows and enables analysing existing models for possible inaccuracies and inconsistencies supported by a reasoning mechanism based on PITL. Following that, a transformation is developed to map the core modelling components of the standards into the extended PG (PG*) based on the semantics presented by the axiomatic system. A real-life case (from the King’s College hospital accident and emergency (A&E) department’s trauma patient pathway) is considered to validate the framework. It is divided into three patient flows to depict the journey of a patient with significant trauma, arriving at A&E, undergoing a procedure and subsequently discharged. Their staff relied upon the UML-AD and BPMN to model the patient flows. An evaluation of their representation is presented to show the shortfalls of the modelling standards to model patient flows. The last step is to model these patient flows using the developed approach, which is supported by enhanced reasoning and scheduling

Internet enabled modelling of extended manufacturing enterprises using the process based techniques

The paper presents the preliminary results of an ongoing research project on Internet enabled process-based modelling of extended manufacturing enterprises. It is proposed to apply the Open System Architecture for CIM (CIMOSA) modelling framework alongside with object-oriented Petri Net models of enterprise processes and object-oriented techniques for extended enterprises modelling. The main features of the proposed approach are described and some components discussed. Elementary examples of object-oriented Petri Net implementation and real-time visualisation are presented