Debugging Process Algebra Specifications

International audienceDesigning and developing distributed and concurrent applications has always been a tedious and error-prone task. In this context, formal techniques and tools are of great help in order to specify such concurrent systems and detect bugs in the corresponding models. In this paper, we propose a new framework for debugging value-passing process algebra through coverage analysis. We illustrate our approach with LNT, which is a recent specification language designed for formally modelling concurrent systems. We define several coverage notions before showing how to instrument the specification without affecting original behaviors. Our approach helps one to improve the quality of a dataset of examples used for validation purposes, but also to find ill-formed decisions, dead code, and other errors in the specification. We have implemented a tool for automating our debugging approach, and applied it to several real-world case studies in different application areas

Using formal methods to support testing

Formal methods and testing are two important approaches that assist in the development of high quality software. While traditionally these approaches have been seen as rivals, in recent years a new consensus has developed in which they are seen as complementary. This article reviews the state of the art regarding ways in which the presence of a formal specification can be used to assist testing

Doctor of Philosophy

dissertationOver the last decade, cyber-physical systems (CPSs) have seen significant applications in many safety-critical areas, such as autonomous automotive systems, automatic pilot avionics, wireless sensor networks, etc. A Cps uses networked embedded computers to monitor and control physical processes. The motivating example for this dissertation is the use of fault- tolerant routing protocol for a Network-on-Chip (NoC) architecture that connects electronic control units (Ecus) to regulate sensors and actuators in a vehicle. With a network allowing Ecus to communicate with each other, it is possible for them to share processing power to improve performance. In addition, networked Ecus enable flexible mapping to physical processes (e.g., sensors, actuators), which increases resilience to Ecu failures by reassigning physical processes to spare Ecus. For the on-chip routing protocol, the ability to tolerate network faults is important for hardware reconfiguration to maintain the normal operation of a system. Adding a fault-tolerance feature in a routing protocol, however, increases its design complexity, making it prone to many functional problems. Formal verification techniques are therefore needed to verify its correctness. This dissertation proposes a link-fault-tolerant, multiflit wormhole routing algorithm, and its formal modeling and verification using two different methodologies. An improvement upon the previously published fault-tolerant routing algorithm, a link-fault routing algorithm is proposed to relax the unrealistic node-fault assumptions of these algorithms, while avoiding deadlock conservatively by appropriately dropping network packets. This routing algorithm, together with its routing architecture, is then modeled in a process-algebra language LNT, and compositional verification techniques are used to verify its key functional properties. As a comparison, it is modeled using channel-level VHDL which is compiled to labeled Petri-nets (LPNs). Algorithms for a partial order reduction method on LPNs are given. An optimal result is obtained from heuristics that trace back on LPNs to find causally related enabled predecessor transitions. Key observations are made from the comparison between these two verification methodologies

Automated specification-based testing of graphical user interfaces

Tese de doutoramento. Engenharia Electrónica e de Computadores. 2006. Faculdade de Engenharia. Universidade do Porto, Departamento de Informática, Escola de Engenharia. Universidade do Minh

Polymorphonuclear Leucocytes and Protease Inhibitors in the Gingival Crevice

This thesis presents the results of a cross sectional clinical study of the PMN granule markers elastase and lactoferrin in conjunction with the major protease inhibitors alpha 1 antitrypsin and alpha 2 macroglobulin in the gingival crevice. 10 subjects with chronic adult periodontitis were selected. Each subject had GCF collected from a healthy site, a gingivitis site and a periodontitis site. The samples were analysed by ELISA. Analysis of the date confirmed that the sites were separated on the basis of clinical findings. With regard to the PMN granule markers, elastase was not able to discriminate between periodontal sites on the basis of absolute amounts or concentration whereas statistically significant differences were observed in relation to the absolute amount of lactoferrin at healthy and periodontitis sites. The relationship between lactoferrin and elastase changed significantly when comparing healthy and gingivitis sites with periodontitis sites, where a 10-fold decrease in the relative release of elastase was noted. It is proposed that this relationship of PMN granule markers may be a useful indicator of periodontal breakdown. In addition it may indicate basic changes in the dynamics of PMN activity in the gingival crevice in relation to the disease state. With regard to protease inhibitors, alpha 1 antitrypsin increased significantly in absolute amounts at sites of inflammation but remained unchanged in relation to its concentration. Alpha 2 macroglobulin increased at sites of inflammation in absolute amounts and was at highest concentration at sites of gingivitis. At sites of inflammation the amount of protease inhibitor relative to elastase increased. Thus, there was no evidence of a defective, host related protease inhibitor mechanism

Formal verification of automotive embedded UML designs

Software applications are increasingly dominating safety critical domains. Safety critical domains are domains where the failure of any application could impact human lives. Software application safety has been overlooked for quite some time but more focus and attention is currently directed to this area due to the exponential growth of software embedded applications. Software systems have continuously faced challenges in managing complexity associated with functional growth, flexibility of systems so that they can be easily modified, scalability of solutions across several product lines, quality and reliability of systems, and finally the ability to detect defects early in design phases. AUTOSAR was established to develop open standards to address these challenges. ISO-26262, automotive functional safety standard, aims to ensure functional safety of automotive systems by providing requirements and processes to govern software lifecycle to ensure safety. Each functional system needs to be classified in terms of safety goals, risks and Automotive Safety Integrity Level (ASIL: A, B, C and D) with ASIL D denoting the most stringent safety level. As risk of the system increases, ASIL level increases and the standard mandates more stringent methods to ensure safety. ISO-26262 mandates that ASILs C and D classified systems utilize walkthrough, semi-formal verification, inspection, control flow analysis, data flow analysis, static code analysis and semantic code analysis techniques to verify software unit design and implementation. Ensuring software specification compliance via formal methods has remained an academic endeavor for quite some time. Several factors discourage formal methods adoption in the industry. One major factor is the complexity of using formal methods. Software specification compliance in automotive remains in the bulk heavily dependent on traceability matrix, human based reviews, and testing activities conducted on either actual production software level or simulation level. ISO26262 automotive safety standard recommends, although not strongly, using formal notations in automotive systems that exhibit high risk in case of failure yet the industry still heavily relies on semi-formal notations such as UML. The use of semi-formal notations makes specification compliance still heavily dependent on manual processes and testing efforts. In this research, we propose a framework where UML finite state machines are compiled into formal notations, specification requirements are mapped into formal model theorems and SAT/SMT solvers are utilized to validate implementation compliance to specification. The framework will allow semi-formal verification of AUTOSAR UML designs via an automated formal framework backbone. This semi-formal verification framework will allow automotive software to comply with ISO-26262 ASIL C and D unit design and implementation formal verification guideline. Semi-formal UML finite state machines are automatically compiled into formal notations based on Symbolic Analysis Laboratory formal notation. Requirements are captured in the UML design and compiled automatically into theorems. Model Checkers are run against the compiled formal model and theorems to detect counterexamples that violate the requirements in the UML model. Semi-formal verification of the design allows us to uncover issues that were previously detected in testing and production stages. The methodology is applied on several automotive systems to show how the framework automates the verification of UML based designs, the de-facto standard for automotive systems design, based on an implicit formal methodology while hiding the cons that discouraged the industry from using it. Additionally, the framework automates ISO-26262 system design verification guideline which would otherwise be verified via human error prone approaches

Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by- step description

High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material

Molecular Genetic and Functional Characterization of candidate loci for controlling quantitative resistance to the oomycete Phytophthora infestans

Late blight is the most devastating potato disease worldwide caused by the oomycete Phytophthora infestans. Lots of breeding efforts are devoted to improve the field resistance to late blight of potato cultivars. Appearance of new pathotypes of P. infestans and the quantitative phenotype of field resistance make the conventional breeding process difficult. The genetics of inheritance of quantitative resistance is not yet fully understood. Marker assisted selection could help to solve the problem to reliably discriminate resistant from susceptible cultivars. The first part of the thesis was focused on identifying genomic regions responsible for resistance to late blight in two new, independent, tetraploid F1 families �SaKa-Ragis� and �BNA�. DNA markers known from previous studies to be linked to resistance loci in the potato genome were tested in the two families, which had been field evaluated in years 2001 and 2002 for late blight resistance and showed normal distribution of the resistance phenotype, indicating polygenic inheritance in both populations. A �cases� and �controls� study was performed. The �cases� were 23 highly resistant and the �controls� were 23 highly susceptible individuals selected from each F1 family. Both populations were genotyped using SNP, CAPS, SSCP and SCAR markers. Markers significantly linked to QTL (quantitative trait locus) for resistance to P. infestans were found on chromosomes II, IV and V in the �BNA� population and on chromosome X in the �SaKa-Ragis� population. The QTL on chromosome X was further characterized by increasing the marker coverage and SNP haplotype construction for CP105, the most significant marker locus. The second part of the thesis was focused on the most significant and reproducible known QTL for resistance to P. infestans on potato chromosome V. This QTL is part of a hot spot for resistance to pathogens in the potato genome (Gebhardt and Valkonen 2001). A major QTL for plant maturity maps to the same genomic region. A genomic region of about 400 kbp including the R1 gene for resistance to P. infestans has been sequenced to identify positional candidate genes besides the R1 gene family (Ballvora et al. 2002). Two contigs have been assembled, one for the �resistant� homologous chromosome with an introgression from the wild potato species Solanum demissum and the other from the �susceptible� allele (Ballvora et al., in preparation). The two contigs were subjected to Gene Mark- gene prediction software resulting in the annotation of 49 ORFs (open reading frames). Based on putative function assignment, 24 of 49 ORFs were selected for further characterization. The expression of the 24 selected ORFs was analyzed by RT-PCR in cDNAs from leaves uninfected and infected with P. infestans, of two diploid potato genotypes, which were the parents of a population showing a major QTL effect on chromosome V but lacked the R1-gene. For 8 ORFs expression was undetectable in leaves. Four genes were up-regulated upon P. infestans infection. The remaining 12 genes were equally expressed in both infected and uninfected leaves, in different intensities. Furthermore, a genetic approach was pursued for the same QTL on chromosome V in order to narrow down genetically the genomic region in which the gene/genes for resistance to P. infestans and maturity are localized. For this objective, 32 highly resistant and late maturing tetraploid cultivars and 33 highly susceptible and early maturing cultivars were selected. The amplicons at six loci on potato chromosome V were sequenced in the 65 cultivars and analyzed for SNPs. At least one SNP in all six loci were significantly associated with maturity and resistance to P. infestans, suggesting extended linkage disequilibrium in a genetic region of about 8 cM on potato chromosome V