Software Technologies: Applications and Foundations
STAF 2016 Collocated Workshops: DataMod, GCM, HOFM, MELO, SEMS, VeryComp, Vienna Austria, July 4-8, 2016, Revised Selected Papers
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Article
Open AccessCausal analysis of positive Reaction Systems
Cause/effect analysis of complex systems is instrumental in better understanding many natural phenomena. Moreover, formal analysis requires the availability of suitable abstract computational models that someh...
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Chapter and Conference Paper
Farming and Automation. How Professional Visions Change with the Introduction of ICT in Greenhouse Cultivation
With this contribution, we would like to contextualize an IoT and Artificial Intelligence project in the current work practices of greenhouse growers. The project follows the user-centered design process in th...
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Article
Open AccessQuantitative extensions of reaction systems based on SOS semantics
Reaction systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reacti...
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Chapter and Conference Paper
Analysis and Verification of Robustness Properties in Becker-Döring Model
Many biochemical processes in living cells involve clusters of particles. Such processes include protein aggregation and the development of intracellular concentration gradients. To study these mechanisms, we ...
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Article
Open AccessCharacterization and computation of ancestors in reaction systems
In reaction systems, preimages and nth ancestors are sets of reactants leading to the production of a target set of products in either 1 or n steps, respectively. Many computational problems on preimages and ance...
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Chapter and Conference Paper
Analysis of COVID-19 Data with PRISM: Parameter Estimation and SIR Modelling
We propose a pipeline for the stochastic analysis of a SIR model for COVID-19 through the stochastic model checker PRISM. The pipeline consists in: (i) the definition of a modified SIR model, able to include g...
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Chapter and Conference Paper
Exploiting Modularity of SOS Semantics to Define Quantitative Extensions of Reaction Systems
Reaction Systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reacti...
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Chapter and Conference Paper
Classification of Biochemical Pathway Robustness with Neural Networks for Graphs
Dynamical properties of biochemical pathways are often assessed by performing numerical (ODE-based) or stochastic simulations. These methods are often computationally very expensive and require reliable quanti...
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Article
Open AccessA survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
Gene Regulatory Networks (GRNs) represent the interactions among genes regulating the activation of specific cell functionalities, such as reception of (chemical) signals or reaction to environmental changes. ...
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Chapter and Conference Paper
Validation of a Simulation Algorithm for Safety-Critical Human Multitasking
Multitasking has become surprisingly present in our life. This is mostly due to the fact that nowadays most of our activities involve the interaction with one or more devices. In such a context the brain mecha...
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Article
Formal modeling and analysis of safety-critical human multitasking
When a person is concurrently interacting with different systems, the amount of cognitive resources required (cognitive load) could be too high and might prevent some tasks from being completed. When such huma...
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Article
Generalized contexts for reaction systems: definition and study of dynamic causalities
Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that c...
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Chapter and Conference Paper
An Algorithm for Simulating Human Selective Attention
The brain mechanism of selective attention plays a key role in determining the success of a human’s interaction with a device. If the user has to perform concurrent tasks by interacting simultaneously with more t...
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Chapter and Conference Paper
A Computational Model of Internet Addiction Phenomena in Social Networks
Addiction is a complex phenomenon, stemming from environmental, biological and psychological causes. It is defined as a natural response of the body to external stimuli, such as drugs, alcohol, but also job, l...
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Chapter and Conference Paper
Multiset Patterns and Their Application to Dynamic Causalities in Membrane Systems
In this paper we investigate dynamic causalities in membrane systems by proposing the concept of “predictor”, originally defined in the context of Ehrenfeucht and Rozemberg’s reaction systems. The goal is to c...
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Chapter and Conference Paper
An Executable Formal Framework for Safety-Critical Human Multitasking
When a person is concurrently interacting with different systems, the amount of cognitive resources required (cognitive load) could be too high and might prevent some tasks from being completed. When such huma...
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Chapter and Conference Paper
Computing Preimages and Ancestors in Reaction Systems
In reaction systems, preimages and n-th ancestors are sets of reactants leading to the production of a target set of products in either one or n steps, respectively. Many computational problems on preimages and a...
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Chapter and Conference Paper
Formalizing a Notion of Concentration Robustness for Biochemical Networks
The main goal of systems biology is to understand the dynamical properties of biological systems by investigating the interactions among the components of a biological system. In this work, we focus on the rob...
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Chapter and Conference Paper
Applications of P Systems in Population Biology and Ecology: The Cases of MPP and APP Systems
We describe two extensions of P systems for the modelling of populations and ecosystems. They are the Minimal Probabilistic P systems (MPP systems) and the Attributed Probabilistic P systems (APP systems). We ...
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Book and Conference Proceedings
