The development of hard real-time systems using a formal approach

Hard real-time systems are a class of computer control systems that must react to demands of their environment by providing `correct' and timely responses. Since these systems are increasingly being used in systems with safety implications, it is crucial that they are designed and developed to operate in a correct manner. This thesis is concerned with developing formal techniques that allow the specification, verification and design of hard real-time systems. Formal techniques for hard real-time systems must be capable of capturing the system's functional and performance requirements, and previous work has proposed a number of techniques which range from the mathematically intensive to those with some mathematical content. This thesis develops formal techniques that contain both an informal and a formal component because it is considered that the informality provides ease of understanding and the formality allows precise specification and verification. Specifically, the combination of Petri nets and temporal logic is considered for the specification and verification of hard real-time systems. Approaches that combine Petri nets and temporal logic by allowing a consistent translation between each formalism are examined. Previously, such techniques have been applied to the formal analysis of concurrent systems. This thesis adapts these techniques for use in the modelling, design and formal analysis of hard real-time systems. The techniques are applied to the problem of specifying a controller for a high-speed manufacturing system. It is shown that they can be used to prove liveness and safety properties, including qualitative aspects of system performance. The problem of verifying quantitative real-time properties is addressed by developing a further technique which combines the formalisms of timed Petri nets and real-time temporal logic. A unifying feature of these techniques is the common temporal description of the Petri net. A common problem with Petri net based techniques is the complexity problems associated with generating the reachability graph. This thesis addresses this problem by using concurrency sets to generate a partial reachability graph pertaining to a particular state. These sets also allows each state to be checked for the presence of inconsistencies and hazards. The problem of designing a controller for the high-speed manufacturing system is also considered. The approach adopted mvolves the use of a model-based controller: This type of controller uses the Petri net models developed, thus preservIng the properties already proven of the controller. It. also contains a model of the physical system which is synchronised to the real application to provide timely responses. The various way of forming the synchronization between these processes is considered and the resulting nets are analysed using concurrency sets.

A novel near real-time quality-control procedure for radiometric profiles measured by Bio-Argo floats: protocols and performances

An array of Bio-Argo floats equipped with radiometric sensors has been recently deployed in various open ocean areas representative of the diversity of trophic and bio-optical conditions prevailing in the so-called Case 1 waters. Around solar noon and almost everyday, each float acquires 0-250 m vertical profiles of Photosynthetically Available Radiation and downward irradiance at three wavelengths (380, 412 and 490 nm). Up until now, more than 6500 profiles for each radiometric channel have been acquired. As these radiometric data are collected out of operator’s control and regardless of meteorological conditions, specific and automatic data processing protocols have to be developed. Here, we present a data quality-control procedure aimed at verifying profile shapes and providing near real-time data distribution. This procedure is specifically developed to: 1) identify main issues of measurements (i.e. dark signal, atmospheric clouds, spikes and wave-focusing occurrences); 2) validate the final data with a hierarchy of tests to ensure a scientific utilization. The procedure, adapted to each of the four radiometric channels, is designed to flag each profile in a way compliant with the data management procedure used by the Argo program. Main perturbations in the light field are identified by the new protocols with good performances over the whole dataset. This highlights its potential applicability at the global scale. Finally, the comparison with modeled surface irradiances allows assessing the accuracy of quality-controlled measured irradiance values and identifying any possible evolution over the float lifetime due to biofouling and instrumental drift.

A novel near real-time quality-control procedure for radiometric profiles measured by Bio-Argo floats: protocols and performances

An array of Bio-Argo floats equipped with radiometric sensors has been recently deployed in various open ocean areas representative of the diversity of trophic and bio-optical conditions prevailing in the so-called Case 1 waters. Around solar noon and almost everyday, each float acquires 0-250 m vertical profiles of Photosynthetically Available Radiation and downward irradiance at three wavelengths (380, 412 and 490 nm). Up until now, more than 6500 profiles for each radiometric channel have been acquired. As these radiometric data are collected out of operator’s control and regardless of meteorological conditions, specific and automatic data processing protocols have to be developed. Here, we present a data quality-control procedure aimed at verifying profile shapes and providing near real-time data distribution. This procedure is specifically developed to: 1) identify main issues of measurements (i.e. dark signal, atmospheric clouds, spikes and wave-focusing occurrences); 2) validate the final data with a hierarchy of tests to ensure a scientific utilization. The procedure, adapted to each of the four radiometric channels, is designed to flag each profile in a way compliant with the data management procedure used by the Argo program. Main perturbations in the light field are identified by the new protocols with good performances over the whole dataset. This highlights its potential applicability at the global scale. Finally, the comparison with modeled surface irradiances allows assessing the accuracy of quality-controlled measured irradiance values and identifying any possible evolution over the float lifetime due to biofouling and instrumental drift.

Near-real-time service provision during effusive crises at Etna and Stromboli: basis and implementation of satellite-based IR operations

Using the NEODAAS-Dundee AVHRR receiving station (Scotland), NEODAAS-Plymouth can provide calibrated brightness temperature data to end users or interim users in near-real time. Between 2000 and 2009 these data were used to undertake volcano hot spot detection, reporting and time-average discharge rate dissemination during effusive crises at Mount Etna and Stromboli (Italy). Data were passed via FTP, within an hour of image generation, to the hot spot detection system maintained at Hawaii Institute of Geophysics and Planetology (HIGP, University of Hawaii at Manoa, Honolulu, USA). Final product generation and quality control were completed manually at HIGP once a day, so as to provide information to onsite monitoring agencies for their incorporation into daily reporting duties to Italian Civil Protection. We here describe the processing and dissemination chain, which was designed so as to provide timely, useable, quality-controlled and relevant information for ‘one voice’ reporting by the responsible monitoring agencies.

Near-real-time service provision during effusive crises at Etna and Stromboli: basis and implementation of satellite-based IR operations

Using the NEODAAS-Dundee AVHRR receiving station (Scotland), NEODAAS-Plymouth can provide calibrated brightness temperature data to end users or interim users in near-real time. Between 2000 and 2009 these data were used to undertake volcano hot spot detection, reporting and time-average discharge rate dissemination during effusive crises at Mount Etna and Stromboli (Italy). Data were passed via FTP, within an hour of image generation, to the hot spot detection system maintained at Hawaii Institute of Geophysics and Planetology (HIGP, University of Hawaii at Manoa, Honolulu, USA). Final product generation and quality control were completed manually at HIGP once a day, so as to provide information to onsite monitoring agencies for their incorporation into daily reporting duties to Italian Civil Protection. We here describe the processing and dissemination chain, which was designed so as to provide timely, useable, quality-controlled and relevant information for ‘one voice’ reporting by the responsible monitoring agencies.

Multiplex real-time PCR monitoring of intestinal helminths in humans reveals widespread polyparasitism in Northern Samar, the Philippines

The global socioeconomic importance of helminth parasitic disease is underpinned by the considerable clinical impact on millions of people. While helminth polyparasitism is considered common in the Philippines, little has been done to survey its extent in endemic communities. High morphological similarity of eggs between related species complicates conventional microscopic diagnostic methods which are known to lack sensitivity, particularly in low intensity infections. Multiplex quantitative PCR diagnostic methods can provide rapid, simultaneous identification of multiple helminth species from a single stool sample. We describe a multiplex assay for the differentiation of Ascaris lumbricoides, Necator americanus, Ancylostoma, Taenia saginata and Taenia solium, building on our previously published findings for Schistosoma japonicum. Of 545 human faecal samples examined, 46.6% were positive for at least three different parasite species. High prevalences of S. japonicum (90.64%), A. lumbricoides (58.17%), T. saginata (42.57%) and A. duodenale (48.07%) were recorded. Neither T. solium nor N. americanus were found to be present. The utility of molecular diagnostic methods for monitoring helminth parasite prevalence provides new information on the extent of polyparasitism in the Philippines municipality of Palapag. These methods and findings have potential global implications for the monitoring of neglected tropical diseases and control measures.

Development of a real time Image analysis system for traffic monitoring applications.

Image processing offers unparalleled potential for traffic monitoring and control. For many years engineers have attempted to perfect the art of automatic data abstraction from sequences of video images. This paper outlines a research project undertaken at Napier University by the authors in the field of image processing for automatic traffic analysis. A software based system implementing TRIP algorithms to count cars and measure vehicle speed has been developed by members of the Transport Engineering Research Unit (TERU) at the University. The TRIP algorithm has been ported and evaluated on an IBM PC platform with a view to hardware implementation of the pre-processing routines required for vehicle detection. Results show that a software based traffic counting system is realisable for single window processing. Due to the high volume of data required to be processed for full frames or multiple lanes, system operations in real time are limited. Therefore specific hardware is required to be designed. The paper outlines a hardware design for implementation of inter-frame and background differencing, background updating and shadow removal techniques. Preliminary results showing the processing time and counting accuracy for the routines implemented in software are presented and a real time hardware pre-processing architecture is described.

Recommendations for in-situ data Near Real Time Quality Control

With the construction of operational oceanography systems, the need for real-time has become more and more important. A lot of work had been done in the past, within National Data Centres (NODC) and International Oceanographic Data and Information Exchange (IODE) to standardise delayed mode quality control procedures. Concerning such quality control procedures applicable in real-time (within hours to a maximum of a week from acquisition), which means automatically, some recommendations were set up for physical parameters but mainly within projects without consolidation with other initiatives. During the past ten years the EuroGOOS community has been working on such procedures within international programs such as Argo, OceanSites or GOSUD, or within EC projects such as Mersea, MFSTEP, FerryBox, ECOOP, and MyOcean. In collaboration with the FP7 SeaDataNet project that is standardizing the delayed mode quality control procedures in NODCs, and MyOcean GMES FP7 project that is standardizing near real time quality control procedures for operational oceanography purposes, the DATA-MEQ working group decided to put together this document to summarize the recommendations for near real-time QC procedures that they judged mature enough to be advertised and recommended to EuroGOOS.

Real-Time PCR Assays for the Detection of Puccinia psidii

Puccinia psidii (Myrtle rust) is an emerging pathogen that has a wide host range in the Myrtaceae family; it continues to show an increase in geographic range and is considered to be a significant threat to Myrtaceae plants worldwide. In this study, we describe the development and validation of three novel real-time polymerase reaction (qPCR) assays using ribosomal DNA and β-tubulin gene sequences to detect P. psidii. All qPCR assays were able to detect P. psidii DNA extracted from urediniospores and from infected plants, including asymptomatic leaf tissues. Depending on the gene target, qPCR was able to detect down to 0.011 pg of P. psidii DNA. The most optimum qPCR assay was shown to be highly specific, repeatable, and reproducible following testing using different qPCR reagents and real-time PCR platforms in different laboratories. In addition, a duplex qPCR assay was developed to allow coamplification of the cytochrome oxidase gene from host plants for use as an internal PCR control. The most optimum qPCR assay proved to be faster and more sensitive than the previously published nested PCR assay and will be particularly useful for high-throughput testing and to detect P. psidii at the early stages of infection, before the development of sporulating rust pustules.

Development of a Real Time System in Algol 68.

For various reasons, many Algol 68 compilers do not directly implement the parallel processing operations defined in the Revised Algol 68 Report. It is still possible however, to perform parallel processing, multitasking and simulation provided that the implementation permits the creation of a master routine for the coordination and initiation of processes under its control. The package described here is intended for real time applications and runs in conjunction with the Algol 68R system; it extends and develops the original Algol 68RT package, which was designed for use with multiplexers at the Royal Radar Establishment, Malvern. The facilities provided, in addition to the synchronising operations, include an interface to an ICL Communications Processor enabling the abstract processes to be realised as the interaction of several teletypes or visual display units with a real time program providing a useful service.

Analysis and control of transient spectra using time-dependent density functional theory.

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INTEGRATED THRESHOLD-ACTIVATED FEEDBACK MICROSYSTEM FOR REAL-TIME CHARACTERIZATION, SENSING AND TREATMENT OF BACTERIAL BIOFILMS

Biofilms are the primary cause of clinical bacterial infections and are impervious to typical amounts of antibiotics, necessitating very high doses for treatment. Therefore, it is highly desirable to develop new alternate methods of treatment that can complement or replace existing approaches using significantly lower doses of antibiotics. Current standards for studying biofilms are based on end-point studies that are invasive and destroy the biofilm during characterization. This dissertation presents the development of a novel real-time sensing and treatment technology to aid in the non-invasive characterization, monitoring and treatment of bacterial biofilms. The technology is demonstrated through the use of a high-throughput bifurcation based microfluidic reactor that enables simulation of flow conditions similar to indwelling medical devices. The integrated microsystem developed in this work incorporates the advantages of previous in vitro platforms while attempting to overcome some of their limitations. Biofilm formation is extremely sensitive to various growth parameters that cause large variability in biofilms between repeated experiments. In this work we investigate the use of microfluidic bifurcations for the reduction in biofilm growth variance. The microfluidic flow cell designed here spatially sections a single biofilm into multiple channels using microfluidic flow bifurcation. Biofilms grown in the bifurcated device were evaluated and verified for reduced biofilm growth variance using standard techniques like confocal microscopy. This uniformity in biofilm growth allows for reliable comparison and evaluation of new treatments with integrated controls on a single device. Biofilm partitioning was demonstrated using the bifurcation device by exposing three of the four channels to various treatments. We studied a novel bacterial biofilm treatment independent of traditional antibiotics using only small molecule inhibitors of bacterial quorum sensing (analogs) in combination with low electric fields. Studies using the bifurcation-based microfluidic flow cell integrated with real-time transduction methods and macro-scale end-point testing of the combination treatment showed a significant decrease in biomass compared to the untreated controls and well-known treatments such as antibiotics. To understand the possible mechanism of action of electric field-based treatments, fundamental treatment efficacy studies focusing on the effect of the energy of the applied electrical signal were performed. It was shown that the total energy and not the type of the applied electrical signal affects the effectiveness of the treatment. The linear dependence of the treatment efficacy on the applied electrical energy was also demonstrated. The integrated bifurcation-based microfluidic platform is the first microsystem that enables biofilm growth with reduced variance, as well as continuous real-time threshold-activated feedback monitoring and treatment using low electric fields. The sensors detect biofilm growth by monitoring the change in impedance across the interdigitated electrodes. Using the measured impedance change and user inputs provided through a convenient and simple graphical interface, a custom-built MATLAB control module intelligently switches the system into and out of treatment mode. Using this self-governing microsystem, in situ biofilm treatment based on the principles of the bioelectric effect was demonstrated by exposing two of the channels of the integrated bifurcation device to low doses of antibiotics.

Copernicus In Situ TAC, Real Time Quality Control for WAVES

In April 2017, CMEMS plans to launch the WAVES NRT products. This document is focused in the automatic RTQC of the collected wave data. The validation procedure includes the delayed mode quality control of the data and will be specified in another guideline. To perform any kind of quality control to wave data, first it’s necessary to know the nature of the measurements and the analysis performed to those measurements to obtain the wave parameters. For that reason next chapter is dedicated to show the usual wave analysis and the different parameters and estimators obtained.

REAL TIME FUZZY CONTROLLER FOR QUADROTOR STABILITY CONTROL

In this report, we develop an intelligent adaptive neuro-fuzzy controller by using adaptive neuro fuzzy inference system (ANFIS) techniques. We begin by starting with a standard proportional-derivative (PD) controller and use the PD controller data to train the ANFIS system to develop a fuzzy controller. We then propose and validate a method to implement this control strategy on commercial off-the-shelf (COTS) hardware. An analysis is made into the choice of filters for attitude estimation. These choices are limited by the complexity of the filter and the computing ability and memory constraints of the micro-controller. Simplified Kalman filters are found to be good at estimation of attitude given the above constraints. Using model based design techniques, the models are implemented on an embedded system. This enables the deployment of fuzzy controllers on enthusiast-grade controllers. We evaluate the feasibility of the proposed control strategy in a model-in-the-loop simulation. We then propose a rapid prototyping strategy, allowing us to deploy these control algorithms on a system consisting of a combination of an ARM-based microcontroller and two Arduino-based controllers. We then use a combination of the code generation capabilities within MATLAB/Simulink in combination with multiple open-source projects in order to deploy code to an ARM CortexM4 based controller board. We also evaluate this strategy on an ARM-A8 based board, and a much less powerful Arduino based flight controller. We conclude by proving the feasibility of fuzzy controllers on Commercial-off the shelf (COTS) hardware, we also point out the limitations in the current hardware and make suggestions for hardware that we think would be better suited for memory heavy controllers.

An inter-laboratory validation of a real time PCR assay to measure host excretion of bacterial pathogens, particularly of Mycobacterium bovis

Advances in the diagnosis of Mycobacterium bovis infection in wildlife hosts may benefit the development of sustainable approaches to the management of bovine tuberculosis in cattle. In the present study, three laboratories from two different countries participated in a validation trial to evaluate the reliability and reproducibility of a real time PCR assay in the detection and quantification of M. bovis from environmental samples. The sample panels consisted of negative badger faeces spiked with a dilution series of M. bovis BCG Pasteur and of field samples of faeces from badgers of unknown infection status taken from badger latrines in areas with high and low incidence of bovine TB (bTB) in cattle. Samples were tested with a previously optimised methodology. The experimental design involved rigorous testing which highlighted a number of potential pitfalls in the analysis of environmental samples using real time PCR. Despite minor variation between operators and laboratories, the validation study demonstrated good concordance between the three laboratories: on the spiked panels, the test showed high levels of agreement in terms of positive/negative detection, with high specificity (100%) and high sensitivity (97%) at levels of 10(5) cells g(-1) and above. Quantitative analysis of the data revealed low variability in recovery of BCG cells between laboratories and operators. On the field samples, the test showed high reproducibility both in terms of positive/negative detection and in the number of cells detected, despite low numbers of samples identified as positive by any laboratory. Use of a parallel PCR inhibition control assay revealed negligible PCR-interfering chemicals co-extracted with the DNA. This is the first example of a multi-laboratory validation of a real time PCR assay for the detection of mycobacteria in environmental samples. Field studies are now required to determine how best to apply the assay for population-level bTB surveillance in wildlife.