A new dialect of SOFL-Syntax formal semantics and tool support

Structured Object Orientated Formal Language (SOFL) is a formal method design methodology that combines data flows diagrams and predicates in order to describe processes that can be refined. This methodology creates a very versatile method of describing a system, which system properties can be proven rigorously. Data flows are grouped by ports that define from which data flows data can be consumed or on which flows data can be generated. For predicates, Logic of Partial Functions (LFP) are used; and an undefined element that is also used to indicate if a data flows do not contain any data. Over time SOFL “evolved organically” and a number of features were added: usability was the main consideration for a feature being added. For a formal language to be useful there must be no uncertainty of a specific design’s meaning. With SOFL, there is a possible contradiction between the requirement that a process's precondition must be true when the process fire, and the fire rules. This contradiction is due to the use of LPF. Semantics (the meaning) of SOFL was not always updated to keep track of the changes made to SOFL which resulted in an outdated and incomplete semantic. The incompleteness of the semantics is a significant factor motivating the work done in this dissertation. In this dissertation, a dialect of SOFL is created to define a semantic. Not all the elements of SOFL are added in order that a simpler semantic can be defined. Elements that were removed include: LPF, Classes, and Non-deterministic broadcast nodes. Semantics of the dialect is created by a two-step process: firstly, an intuitive understanding of the dialect is created, and secondly, both static and dynamic semantics are defined by means of translations. A translation is a mapping from the dialect to a formal language that describes a certain aspect of the dialect. Static semantics defines the meaning of the elements that are “fixed” in their state: SMT-LIB is used as the target language to describe the static semantics of the dialect. Dynamic semantics describes how an element in a design changes over time: the process algebra mCRL2 is used as the formal language which describes the dynamic behaviour of the dialect. The SMT-Solver Z3 and tools included in mCLR2 are used to analyse the translation of the dialect. Use of these tools allows properties that are necessary for a design to have a well defined meaning, to be proven. Properties that can be proven include: a process can fire, a process can fire an infinite number of times, and a predicate that described a property. An Eclipse plug-in is created so that translation is not required to be done manually. After a design is translated the tools Z3 and mCRL2 are run using script files and the results of the analysis are displayed on the screen. The desired properties could be proven but for a moderate size design, but as the size of the design increased the analysis of the translation could not be completed due to computational problem. Usability of the tool can be improved by not only using a textual representation of a design, but also visual representations as in SOFL. As a result, properties that are necessary for a design to have a well-defined meaning, can be proven using these tools.Dissertation (MSc)--University of Pretoria, 2018.Computer ScienceMScUnrestricte

Fail-Safe Test Generation of Safety Critical Systems

This dissertation introduces a technique for testing proper failure mitigation in safety critical systems. Unlike other approaches which integrate behavioral and failure models, and then generate tests from the integrated model, we build safety mitigation tests from an existing behavioral test suite, using an explicit mitigation model for which we generate mitigation paths which are then woven at selected failure points into the original test suite to create failure-mitigation tests (safety mitigation test)

Measurement of bioprocess containment by quantitative polymerase chain reaction

This thesis describes the development and application of a method for the measurement of the release of genetically modified micro-organisms from large scale bioprocesses. Polymerase chain reaction (PCR) assays for two E. coli K-12 strains have been shown to be specific for the target strain and have sufficiently low limits of detection (less than 50 cells per PCR) for monitoring of bioprocess release. A quantitative PCR assay, using a competitive internal standard, for one E. coli strain allows measurement of the concentration of the bacteria over a range of up to 6 orders of magnitude with a measurement error of ±0.11 logs. This method has been applied to samples taken from an Aerojet General Cyclone air sampling device allowing the determination of the number of whole cells of the target organism in a sampled aerosol. Using this method, good correlation has been observed between the number of cells released by atomisation into a fixed, contained volume and the number of cells captured and enumerated. Aspects of large scale fermentation, homogenisation and centrifugation unit operations have been studied to determine the effectiveness of their containment. Airborne release of process micro-organisms has been detected in some instances, but the scale of the release was generally found to be small considering the total biomass involved in the bioprocess. Implications of the methodology and the findings from model and case studies on current engineering practice and bioprocess risk assessment are discussed. Areas for further improvement of the method and applications outside of bioprocess containment validation are identified

A record of research directed towards enhancement of the safety of clinical anaesthesia

Clinical Anaesthesia is an indispensable adjunct to the surgical treatment of disease. It directly affects the lives of a great number of people since every year no fewer than one in every twenty-five persons in the population is required to undergo a procedure which necessitates it. Of itself non-therapeutic, clinical anaesthesia must, above all else. be safe for the patient. Any adverse outcome to clinical anaesthesia and factors relevant to its administration results, at best, in postoperative morbidity for the patient and, at worst, his demise. Identification and examination of the factors and circumstances which have a material influence on the safety of anaesthesia for the patient, provided the motivation for and is the central theme of this collection of research publications which was submitted to the University of Cape Town in fulfilment of the requirements for the award of the Degree of Doctor of Science (Medicine). The publications submitted report the results of forty years of endeavour. In terms of their subject matter, these publications may be broadly grouped into the following five fields of interest: - 1) The Epidemiology of Death Attributable to Anaesthesia. 2) Pharmacogenetic States of concern to the Anaesthetist - a) The Malignant Hyperthermia Myopathy. b) The Acute Porphyrias. 3) The Effects of Anaesthetics on the Liver - Studies of Hepatic Drug Metabolism of relevance to post-Halothane Hepatitis and the hepatotoxicity of anaesthetic agents. b) The treatment of Fulminant Liver Failure. 4) Heat Homeostasis during Anaesthesia - a) Inadvertent Hypothermia during anaesthesia. b) Induced Hypothermia during anaesthesia. 5) Miscellaneous. Within these fields of interest, papers have been grouped in terms of related aspects of the main topic they cover. Editorial comment is included where appropriate. The nature and scope of many of the above investigations was such as to require, for their satisfactory conclusion, collaborative interdisciplinary research combining the endeavours of other clinicians and paramedical scientists. Appropriate recognition of such collaboration has resulted in the multiple authorship registered for many of the publications in this collection

Casco Bay Weekly : 26 September 1991

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