Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Modeling IoT-aware Business Processes - A State of the Art Report

This research report presents an analysis of the state of the art of modeling Internet of Things (IoT)-aware business processes. IOT links the physical world to the digital world. Traditionally, we would find information about events and processes in the physical world in the digital world entered by humans and humans using this information to control the physical world. In the IoT paradigm, the physical world is equipped with sensors and actuators to create a direct link with the digital world. Business processes are used to coordinate a complex environment including multiple actors for a common goal, typically in the context of administrative work. In the past few years, we have seen research efforts on the possibilities to model IoT- aware business processes, extending process coordination to real world entities directly. This set of research efforts is relatively small when compared to the overall research effort into the IoT and much of the work is still in the early research stage. To create a basis for a bridge between IoT and BPM, the goal of this report is to collect and analyze the state of the art of existing frameworks for modeling IoT-aware business processes.Comment: 42 page

Advanced Techniques for Assets Maintenance Management

16th IFAC Symposium on Information Control Problems in Manufacturing INCOM 2018 Bergamo, Italy, 11–13 June 2018. Edited by Marco Macchi, László Monostori, Roberto PintoThe aim of this paper is to remark the importance of new and advanced techniques supporting decision making in different business processes for maintenance and assets management, as well as the basic need of adopting a certain management framework with a clear processes map and the corresponding IT supporting systems. Framework processes and systems will be the key fundamental enablers for success and for continuous improvement. The suggested framework will help to define and improve business policies and work procedures for the assets operation and maintenance along their life cycle. The following sections present some achievements on this focus, proposing finally possible future lines for a research agenda within this field of assets management

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

Reliability demonstration for safety-critical systems

This paper suggests a new model for reliability demonstration of safety-critical systems, based on the TRW Software Reliability Theory. The paper describes the model; the test equipment required and test strategies based on the various constraints occurring during software development. The paper also compares a new testing method, Single Risk Sequential Testing (SRST), with the standard Probability Ratio Sequential Testing method (PRST), and concludes that: • SRST provides higher chances of success than PRST • SRST takes less time to complete than PRST • SRST satisfies the consumer risk criterion, whereas PRST provides a much smaller consumer risk than the requirement

Construction and Verification of Performance and Reliability Models

Over the last two decades formal methods have been extended towards performance and reliability evaluation. This paper tries to provide a rather intuitive explanation of the basic concepts and features in this area. Instead of striving for mathematical rigour, the intention is to give an illustrative introduction to the basics of stochastic models, to stochastic modelling using process algebra, and to model checking as a technique to analyse stochastic models

Evaluation of Intelligent Intrusion Detection Models

This paper discusses an evaluation methodology that can be used to assess the performance of intelligent techniques at detecting, as well as predicting, unauthorised activities in networks. The effectiveness and the performance of any developed intrusion detection model will be determined by means of evaluation and validation. The evaluation and the learning prediction performance for this task will be discussed, together with a description of validation procedures. The performance of developed detection models that incorporate intelligent elements can be evaluated using well known standard methods, such as matrix confusion, ROC curves and Lift charts. In this paper these methods, as well as other useful evaluation approaches, are discussed.Peer reviewe