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Petri Net is a formalism to describe changes between 2 or more states across discrete time and has been used to model many systems. We present PNet - a pure Python library for Petri Net modeling and simulation in Python programming…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
Petri nets have found widespread use among many application domains, not least due to their human-friendly graphical syntax for the composition of interacting distributed and asynchronous processes and services, based in partial-order…
Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…
Process mining is concerned with deriving formal models capable of reproducing the behaviour of a given organisational process by analysing observed executions collected in an event log. The elements of an event log are finite sequences…
The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction…
Single trial analyses of ensemble activity in alert animals demonstrate that cortical circuits dynamics evolve through temporal sequences of metastable states. Metastability has been studied for its potential role in sensory coding, memory…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
Nowadays, with the emergence and the evolution of new technologies, such as e-business, a large number of companies are connected to Internet, and have proposed web services to trade. Web services as presented, are conceptually limited…
This paper is devoted to the use of hybrid Petri nets (PNs) for modeling and control of hybrid dynamic systems (HDS). Modeling, analysis and control of HDS attract ever more of researchers' attention and several works have been devoted to…
Round-the-clock monitoring of human behavior and emotions is required in many healthcare applications which is very expensive but can be automated using machine learning (ML) and sensor technologies. Unfortunately, the lack of…
In a previous paper we introduced immediate observation (IO) Petri nets, a class of interest in the study of population protocols and enzymatic chemical networks. In the first part of this paper we show that IO nets are globally flat, and…
Finite-state models are widely used in software engineering, especially in control systems development. Commonly, in control applications such models are developed manually, hence, keeping them up-to-date requires extra effort. To simplify…
Petri Nets (PN) are a central, theoretically sound model for concurrent or distributed systems but, at least in their classical definition, not expressive enough to represent dynamic reconfiguration capabilities. On the other side,…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
The growing complexity of the power grid, driven by increasing share of distributed energy resources and by massive deployment of intelligent internet-connected devices, requires new modelling tools for planning and operation. Physics-based…
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators…
Modelling, specifying and reasoning about complex systems requires to process in an integrated fashion declarative and procedural aspects of the target domain. The paper reports on an experiment conducted with a propositional version of…
In Petri net synthesis we ask whether a given transition system $A$ can be implemented by a Petri net $N$. Depending on the level of accuracy, there are three ways how $N$ can implement $A$: an embedding, the least accurate implementation,…
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…