Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Exploring Teacher Candidates’ Perception of Practicum Placement Within Concurrent Teacher Education in Two Ontario Universities

In this study, teacher candidates’ perception of their concurrent education program at two Ontario universities were examined, with specific emphasis on how the programs utilized practicum placements, to determine the effectiveness in preparing teacher candidates to teach. This research also strived to uncover the best ways to optimize concurrent teacher education through practicum placements. A questionnaire and interviews were used to uncover teacher candidates’ perceptions at one teacher education program that used full integration of practicum and one that used minimal integration of practicum. The findings revealed that teacher candidates were generally more satisfied with the overall program when there was full integration of practicum. There were statistically significant differences found between the two concurrent programs with regard to practicum time and preparedness and context of the practicum and a highly significant difference found for theory-practice divide. There was also a statistically significant difference (p < .05) observed between the teacher candidates at each university in terms of their beliefs about the need for improvement of their program. Some of the improvements that participants believed could be made to their respective programs included having (a) exceptional mentor teachers and teacher educators, (b) longer placements with a balance of observation and practicum teaching, (c) clear expectations and evaluations of practicum placement, and (d) more distinct connections between theory and practice made within the programs.