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We provide code for the calculation of the laser beam quality "M2" using our covariance method and its comparison to the ISO 11146. This is the code for the following reference M. H. Griessmann, A. C. Martinez-Becerril, and J. S. Lundeen, "Method to determine the M2 beam quality from the electric field in a single plane," Opt. Continuum 2, 1833-1848 (2023).

Enables extraction of morphomic markers from CT images by non-technically skilled clinicians.

iQcell is a platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data.

Tigmint is a tool for correcting misassemblies in genome assembly drafts using linked or long sequencing reads

This is an example capsule for CoBE(https://www.pmcobe.ca) executable. The capsule is made using software, source code and data coming from public sources and other authors. Please find the original links for code/data in capsule description below: https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0129-5 https://github.com/LupienLab/VSE

Python code to study the beam steering performance of an optical phased array with pixel limitations.

Visualizing pseudoknots and RNA editing employing compressed tree graphs.

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

While modern building codes have achieved success in preserving life, current code provisions do not explicitly address damage caused by earthquakes, leading to the prevalence of large economic losses. Examples of this limited scope are the changes made to design provisions for steel moment resisting frames (MRFs) following the 1994 pre-Northridge earthquake, where the pre-qualified connection detailing now prescribed for steel moment resisting frames increases the resistance to collapse but still relies on plastic deformations to dissipate energy, potentially limiting the overall improvement in seismic resiliency when compared to pre-Northridge connections. Since the introduction of these pre-qualified connections, several alternative seismic force resisting systems have been proposed which can reduce the expected economic losses by utilizing innovative energy dissipation methods and self-centering behaviour. However, as the use of these low-damage systems is not prescribed in current codes, their application is limited. This thesis begins by examining the improvements in global performance obtained by implementing two examples of low-damage and high-performance MRF connections: the sliding hinge joint (SHJ) and self-centering sliding hinge joint (SCSHJ). Since the goal of these connections is to increase the seismic resiliency of MRFs, their impact is evaluated using several metrics including exposure to longer duration or aftershock earthquakes, as well as measuring their impact on different engineering demand parameters (EDPs). Once this impact has been established, an efficient design implementation is explored where these connections are placed only at locations with large ductility demands, allowing detailing resources to be concentrated at locations where they will provide the largest benefit. After exploring the global performance measured using engineering demand parameters, the economic and downtime reduction benefits obtained from these low-damage and high-performance connections are compared with alternative upgrade strategies. To help identify the most efficient upgrade strategy, a genetic algorithm is applied to define a methodology for optimizing seismic upgrades, including both structural and non-structural options. The optimization methodology considers the benefits in reductions of economic or downtime losses caused by earthquakes, measured using the performance based earthquake engineering (PBEE) methodology, versus the capital costs required to implement each upgrade. Finally, to aid engineers in selecting upgrades throughout all stages of the design process, this optimization methodology is included as the most advanced stage of a proposed seismic upgrade design framework. In the earlier design stages, the framework relies on a new median shift probability (MSP) method to rapidly summarize the effects of structural upgrades on nonstructural components. While the framework and optimization methodology are demonstrated in this thesis by their application to buildings with steel MRFs, they are easily adaptable to consider multiple objectives, building types, non-structural component populations, and building owners. Overall, this thesis provides insight on both the global performance benefits that can be achieved with the newly developed SHJ and SCSHJ connections, and presents a framework to select and optimize various competing seismic upgrade strategies. Thesis Doctor of Philosophy (PhD) Modern buildings can typically withstand earthquakes without collapsing, but extensive repair or replacement of both the structure and its components are often required after a major event. To reduce these costs, improvements to both the structure and its components are continuously being researched. However, these upgrades can compete with one another for limited available funding, and they are not always independent, with structural changes influencing the demands on non-structural components. In an effort to move toward more optimized and resilient seismic design of buildings with steel moment resisting frames, this thesis begins by examining the effects of two newly proposed low-damage connections and investigates the opportunity to apply these low-damage connections at only specific structural locations to provide the desired performance effects more efficiently. In the second half of the thesis, a comparison of this particular upgrade to several other alternatives is accomplished by developing a framework to identify the upgrades having the largest benefit for the smallest cost by including combinations of modifications to both the structure and its components. The framework includes increasing levels of analytical refinement when evaluating upgrade strategies, providing designers with a more streamlined process to design and evaluate seismic resiliency improvement strategies in structures even beyond those used in this thesis.

This is an example capsule for CoBE(https://www.pmcobe.ca) executable. The capsule is made using software, source code and data coming from public sources and other authors. Please find the original links for code/data in capsule description below: Run Clustering of genomic REgions Analysis Method (CREAM) algorithm on example data. (https://genome.cshlp.org/content/early/2019/09/18/gr.248658.119)