Abstract Cyber-physical systems are complex environments that combine physical devices (i.e., sensors and actuators) with a software controller. The ubiquity of these systems and dangers associated with their failure require the implementation of mechanisms to monitor, verify and guarantee their correct behaviour. This paper presents ParetoLib 2.0, a Python tool for offline monitoring and specification mining of cyber-physical systems. ParetoLib 2.0 uses signal temporal logic (STL) as the formalism for specifying properties on time series. ParetoLib 2.0 builds upon other tools for evaluating and mining STL expressions, and extends them with new functionalities. ParetoLib 2.0 implements a set of new quantitative operators for trace analysis in STL, a novel mining algorithm and an original graphical user interface. Additionally, the performance is optimised with respect to previous releases of the tool via data-type annotations and multi core support. ParetoLib 2.0 allows the offline verification of STL properties as well as the specification mining of parametric STL templates. Thanks to the implementation of the new quantitative operators for STL, the tool outperforms the expressiveness and capabilities of similar runtime monitors.

Abstract In recent years, we have seen many performance fiascos in the deployment of new systems, such as the US health insurance web. This paper describes the functionality and architecture, as well as success stories, of a tool that helps address these types of issues. The tool allows assessing software designs regarding quality, in particular performance and reliability. Starting from a UML design with quality annotations, the tool applies model-transformation techniques to yield analyzable models. Such models are then leveraged by the tool to compute quality metrics. Finally, quality results, over the design, are presented to the engineer, in terms of the problem domain. Hence, the tool is an asset for the software engineer to evaluate system quality through software designs. While leveraging the Eclipse platform, the tool uses UML and the MARTE, DAM and DICE profiles for the system design and the quality modeling.

BACKGROUND: Model checking has been recently introduced as an integrated framework for extracting information of the phylogenetic trees using temporal logics as a querying language, an extension of modal logics that imposes restrictions of a boolean formula along a path of events. The phylogenetic tree is considered a transition system modeling the evolution as a sequence of genomic mutations (we understand mutation as different ways that DNA can be changed), while this kind of logics are suitable for traversing it in a strict and exhaustive way. Given a biological property that we desire to inspect over the phylogeny, the verifier returns true if the specification is satisfied or a counterexample that falsifies it. However, this approach has been only considered over qualitative aspects of the phylogeny. RESULTS: In this paper, we repair the limitations of the previous framework for including and handling quantitative information such as explicit time or probability. To this end, we apply current probabilistic continuous-time extensions of model checking to phylogenetics. We reinterpret a catalog of qualitative properties in a numerical way, and we also present new properties that couldn't be analyzed before. For instance, we obtain the likelihood of a tree topology according to a mutation model. As case of study, we analyze several phylogenies in order to obtain the maximum likelihood with the model checking tool PRISM. In addition, we have adapted the software for optimizing the computation of maximum likelihoods. CONCLUSIONS: We have shown that probabilistic model checking is a competitive framework for describing and analyzing quantitative properties over phylogenetic trees. This formalism adds soundness and readability to the definition of models and specifications. Besides, the existence of model checking tools hides the underlying technology, omitting the extension, upgrade, debugging and maintenance of a software tool to the biologists. A set of benchmarks justify the feasibility of our approach.

The need for general-purpose algorithms for studying biological properties in phylogenetics motivates research into formal verification frameworks. Researchers can focus their efforts exclusively on evolution trees and property specifications. To this end, model checking, a mature automated verification technique originating in computer science, is applied to phylogenetic analysis. Our approach is based on three cornerstones: a logical modeling of the evolution with transition systems; the specification of both phylogenetic properties and trees using flexible temporal logic formulas; and the verification of the latter by means of automated computer tools. The most conspicuous result is the inception of a formal framework which allows for a symbolic manipulation of biological data (based on the codification of the taxa). Additionally, different logical models of evolution can be considered, complex properties can be specified in terms of the logical composition of others, and the refinement of unfulfilled properties as well as the discovery of new properties can be undertaken by exploiting the verification results. Some experimental results using a symbolic model verifier support the feasibility of the approach.