Model Checking Branching Properties on Petri Nets with Transits (Full Version)

To model check concurrent systems, it is convenient to distinguish between the data flow and the control. Correctness is specified on the level of data flow whereas the system is configured on the level of control. Petri nets with transits and Flow-LTL are a corresponding formalism. In Flow-LTL, both the correctness of the data flow and assumptions on fairness and maximality for the control are expressed in linear time. So far, branching behavior cannot be specified for Petri nets with transits. In this paper, we introduce Flow-CTL* to express the intended branching behavior of the data flow while maintaining LTL for fairness and maximality assumptions on the control. We encode physical access control with policy updates as Petri nets with transits and give standard requirements in Flow-CTL*. For model checking, we reduce the model checking problem of Petri nets with transits against Flow-CTL* via automata constructions to the model checking problem of Petri nets against LTL. Thereby, physical access control with policy updates under fairness assumptions for an unbounded number of people can be verified.Comment: 23 pages, 5 figure

IST Austria Thesis

Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency. First, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point

Extracting proofs from documents

Often, theorem checkers like PVS are used to check an existing proof, which is part of some document. Since there is a large difference between the notations used in the documents and the notations used in the theorem checkers, it is usually a laborious task to convert an existing proof into a format which can be checked by a machine. In the system that we propose, the author is assisted in the process of converting an existing proof into the PVS language and having it checked by PVS. 1 Introduction The now-classic ALGOL 60 report [5] recognized three different levels of language: a reference language, a publication language and several hardware representations, whereby the publication language was intended to admit variations on the reference language and was to be used for stating and communicating processes. The importance of publication language ---often referred to nowadays as "pseudo-code"--- is difficult to exaggerate since a publication language is the most effective way..

Foundations of Software Science and Computation Structures

This open access book constitutes the proceedings of the 22nd International Conference on Foundations of Software Science and Computational Structures, FOSSACS 2019, which took place in Prague, Czech Republic, in April 2019, held as part of the European Joint Conference on Theory and Practice of Software, ETAPS 2019. The 29 papers presented in this volume were carefully reviewed and selected from 85 submissions. They deal with foundational research with a clear significance for software science

Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species

Background: Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors. Even though the role of quite a few mosquito salivary proteins has been clarified in the last decade, we still completely ignore the physiological role of many of them as well as the extent of their involvement in the complex interactions taking place between the mosquito vectors, the pathogens they transmit and the vertebrate host. The recent release of the genomes of 16 Anopheles species offered the opportunity to get insights into function and evolution of salivary protein families in anopheline mosquitoes. Results: Orthologues of fifty three Anopheles gambiae salivary proteins were retrieved and annotated from 18 additional anopheline species belonging to the three subgenera Cellia, Anopheles, and Nyssorhynchus. Our analysis included 824 full-length salivary proteins from 24 different families and allowed the identification of 79 novel salivary genes and re-annotation of 379 wrong predictions. The comparative, structural and phylogenetic analyses yielded an unprecedented view of the anopheline salivary repertoires and of their evolution over 100 million years of anopheline radiation shedding light on mechanisms and evolutionary forces that contributed shaping the anopheline sialomes. Conclusions: We provide here a comprehensive description, classification and evolutionary overview of the main anopheline salivary protein families and identify two novel candidate markers of human exposure to malaria vectors worldwide. This anopheline sialome catalogue, which is easily accessible as hyperlinked spreadsheet, is expected to be useful to the vector biology community and to improve the capacity to gain a deeper understanding of mosquito salivary proteins facilitating their possible exploitation for epidemiological and/or pathogen-vector-host interaction studies