Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths (unitigs) in an assembly graph. If one defines a genome assembly solution as a closed arc-covering walk of the graph, then unitigs appear in all solutions, being thus safe partial solutions. All such safe walks were recently characterized as omnitigs, leading to the first safe and complete genome assembly algorithm. Even if omnitig finding was improved to quadratic time, it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs. We describe an O(m)-time algorithm to identify all maximal omnitigs of a graph with n nodes and m arcs, notwithstanding the existence of families of graphs with Θ(mn) total maximal omnitig size. This is based on the discovery of a family of walks (macrotigs) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig, with two consequences: a linear-time output sensitive algorithm enumerating all maximal omnitigs and a compact O(m) representation of all maximal omnitigs. This safe and complete genome assembly algorithm was followed by other works improving the time bounds, as well as extending the results for different notions of assembly solution. But it remained open whether one can be complete also for models of genome assembly of practical applicability. In this dissertation, we also present a universal framework for obtaining safe and complete algorithms which unify the previous results, while also allowing to characterize different assembly problems. This is based on a novel graph structure, called the hydrostructure of a walk, which highlights the reachability properties of the graph from the perspective of the walk. Almost all of our characterizations are directly adaptable to optimal verification algorithms, and simple enumeration algorithms. Most of these algorithms are also improved to optimality using an incremental computation procedure and a previous optimal algorithm of a specific model.

Critical industrial applications in embedded field devices require reliability and consistency. Cloudbased services have been gaining attraction in embedded field devices for monitoring, optimization, predictive maintenance, and other supporting use cases. A significant challenge persists in enabling cloud-connection to the embedded field devices. The central issues on this matter are diversity, resource constraint, and the critical applications of these devices. This paper proposes a novel concept for enabling cloud connection to these devices. A dedicated software module, μConnector, has been introduced for cloud-related activities. It operates on Zephyr RTOS. The purpose of μConnector is to create a separation between critical and cloud related applications within the embedded field devices. μConnector is designed to be application-agnostic while being independent of vendor selection for hardware components. The scientific contribution of the paper lies in the introduction of μConnector. The presented concept addresses the challenges associated with cloud connectivity for embedded field devices. Its primary objective is to define architectural decisions guiding the implementation of the proposed software module.

Ontario’s rock barrens landscape consists of exposed bedrock ridges which host a mosaic of thin lichen- and moss- covered soil patches, forested valleys, beaver ponds, and depressional wetlands. Peat-filled ephemeral wetlands within bedrock depressions act as gatekeepers to hydrological connectivity between their small headwater catchments and the rest of the landscape downstream through strong fill-and-spill dynamics. We developed a water balance model, RHO, with inputs of precipitation and potential evapotranspiration (PET) to better understand the factors impacting water table (WT) and storage dynamics and in turn the hydrological connectivity of ephemeral wetlands. Field surveys were conducted at six wetlands to obtain and determine the variability in measurable site characteristics, in particular the wetland depression morphometry, to parameterize RHO. Three sites were used in a calibration and validation procedure where modelled WTs were compared to measured WT data from the snow-free seasons for each site to determine the best parameter values. We show that RHO is capable of predicting WT dynamics with inputs of precipitation and PET, when parameterized for specific sites. Wildfire disturbance is known to increase the run-off from hillslopes and remove surface organic soils through combustion. To predict the impacts of wildfire disturbance on ephemeral wetland hydrological connectivity, a generic model wetland depression was parameterized in RHO and used to predict the changes in hydrological connectivity under various wildfire scenarios and test the sensitivity of modelled connectedness to impacted parameters. Modelled results show that connectivity increases under all scenarios tested, and that changes to connectivity are primarily due to increases in run-in. Water balance models, like RHO, can be used to better understand the hydrological connectivity of wetlands in a rock barrens landscape. These models are useful in predicting impacts on the hydrological connectivity, and hydrological ecosystem services, from disturbances such as wildfire and can inform future field research experimental designs. / Thesis / Master of Science (MSc) / Rock barrens landscapes provide several important ecosystem services, which are influenced by hydrological flow paths and water storage on the landscape. Central to these hydrological dynamics is the storage and discharge of water in small wetlands which form in bedrock depressions. Here we develop a simple hydrological model to simulate the water storage and discharge of rock barrens wetlands. We then use this model to explore how wildfire disturbance is likely to change the supply of water to the rest of the landscape by simulating several different scenarios and testing which changes in the model have the largest impact on the water supply. We show that wetlands discharge more water after wildfire disturbance, mainly because of increases in run-off from areas upstream of the impacted wetlands. This modelling approach helps us better understand how wildfire is likely to impact the ecosystem services of a rock barrens landscapes.

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