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

An intervention modelling experiment to change GP's intentions to implement evidence-based practice : using theory-based interventions to promote GP management of upper respiratory tract infection without prescribing antibiotics #2

Background: Psychological theories of behaviour may provide a framework to guide the design of interventions to change professional behaviour. Behaviour change interventions, designed using psychological theory and targeting important motivational beliefs, were experimentally evaluated for effects on the behavioural intention and simulated behaviour of GPs in the management of uncomplicated upper respiratory tract infection (URTI). Methods: The design was a 2 × 2 factorial randomised controlled trial. A postal questionnaire was developed based on three theories of human behaviour: Theory of Planned Behaviour; Social Cognitive Theory and Operant Learning Theory. The beliefs and attitudes of GPs regarding the management of URTI without antibiotics and rates of prescribing on eight patient scenarios were measured at baseline and post-intervention. Two theory-based interventions, a "graded task" with "action planning" and a "persuasive communication", were incorporated into the post-intervention questionnaire. Trial groups were compared using co-variate analyses. Results: Post-intervention questionnaires were returned for 340/397 (86%) GPs who responded to the baseline survey. Each intervention had a significant effect on its targeted behavioural belief: compared to those not receiving the intervention GPs completing Intervention 1 reported stronger self-efficacy scores (Beta = 1.41, 95% CI: 0.64 to 2.25) and GPs completing Intervention 2 had more positive anticipated consequences scores (Beta = 0.98, 95% CI = 0.46 to 1.98). Intervention 2 had a significant effect on intention (Beta = 0.90, 95% CI = 0.41 to 1.38) and simulated behaviour (Beta = 0.47, 95% CI = 0.19 to 0.74). Conclusion: GPs' intended management of URTI was significantly influenced by their confidence in their ability to manage URTI without antibiotics and the consequences they anticipated as a result of doing so. Two targeted behaviour change interventions differentially affected these beliefs. One intervention also significantly enhanced GPs' intentions not to prescribe antibiotics for URTI and resulted in lower rates of prescribing on patient scenarios compared to a control group. The theoretical frameworks utilised provide a scientific rationale for understanding how and why the interventions had these effects, improving the reproducibility and generalisability of these findings and offering a sound basis for an intervention in a "real world" trial. Trial registration: Clinicaltrials.gov NCT00376142This study is funded by the European Commission Research Directorate as part of a multi-partner program: Research Based Education and Quality Improvement (ReBEQI): A Framework and tools to develop effective quality improvement programs in European healthcare. (Proposal No: QLRT-2001-00657)

Behavioural equivalences for timed systems

Timed transition systems are behavioural models that include an explicit treatment of time flow and are used to formalise the semantics of several foundational process calculi and automata. Despite their relevance, a general mathematical characterisation of timed transition systems and their behavioural theory is still missing. We introduce the first uniform framework for timed behavioural models that encompasses known behavioural equivalences such as timed bisimulations, timed language equivalences as well as their weak and time-abstract counterparts. All these notions of equivalences are naturally organised by their discriminating power in a spectrum. We prove that this result does not depend on the type of the systems under scrutiny: it holds for any generalisation of timed transition system. We instantiate our framework to timed transition systems and their quantitative extensions such as timed probabilistic systems

Folk Theorems on the Correspondence between State-Based and Event-Based Systems

Kripke Structures and Labelled Transition Systems are the two most prominent semantic models used in concurrency theory. Both models are commonly believed to be equi-expressive. One can find many ad-hoc embeddings of one of these models into the other. We build upon the seminal work of De Nicola and Vaandrager that firmly established the correspondence between stuttering equivalence in Kripke Structures and divergence-sensitive branching bisimulation in Labelled Transition Systems. We show that their embeddings can also be used for a range of other equivalences of interest, such as strong bisimilarity, simulation equivalence, and trace equivalence. Furthermore, we extend the results by De Nicola and Vaandrager by showing that there are additional translations that allow one to use minimisation techniques in one semantic domain to obtain minimal representatives in the other semantic domain for these equivalences.Comment: Full version of SOFSEM 2011 pape

Behavioural Microsimulation Modelling With the Melbourne Institute Tax and Transfer Simulator(MITTS) : Uses and Extensions

This paper describes microsimulation modelling in non-technical terms; and it explains what can be achieved with microsimulation modelling in general, and the Melbourne Institute Tax and Transfer Simulator (MITTS) in particular. The focus is on behavioural microsimulation modelling, which takes individuals’ labour supply responses into account when analysing tax and transfer reforms. Microsimulation models are built to replicate closely the considerable degree of heterogeneity observed in the population. Several examples of recent uses of MITTS are given and briefly described. In addition, one worked-out example is presented to illustrate some of the features and typical outputs of MITTS. Given the relatively recent development of behavioural microsimulation models, there are several opportunities for further extensions. For example, it would be valuable to allow for the demand side of labour, indicating whether new labour force participants are likely to find work; or to allow for life-cycle dynamics, which are important to deal with population-ageing issues or with female labour force participation.

Discrete Simulation of Behavioural Hybrid Process Calculus

Hybrid systems combine continuous-time and discrete behaviours. Simulation is one of the tools to obtain insight in dynamical systems behaviour. Simulation results provide information on performance of system and are helpful in detecting potential weaknesses and errors. Moreover, the results are handy in choosing adequate control strategies and parameters. In our contribution we report a work in progress, a technique for simulation of Behavioural Hybrid Process Calculus, an extension of process algebra that is suitable for the modelling and analysis of hybrid systems