Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS

This is a post-peer-review, pre-copyedit version of an article published in Lecture Notes in Computer Science. The final authenticated version is available online at: https://doi.org/10.1007/978-3-319-09873-9_57[Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. In this work we present EpistSearch, a parallelized tool that, following the log-linear model approach, uses a novel filter to determine the interactions between all SNP-pairs. Our tool is parallelized using a hybrid combination of Pthreads and CUDA in order to take advantage of CPU/GPU architectures. Experimental results with simulated and real datasets show that EpistSearch outperforms previous approaches, either using GPUs or only CPU cores. For instance, an exhaustive analysis of a real-world dataset with 500,000 SNPs and 5,000 individuals requires less than 42 minutes on a machine with 6 CPU cores and a GTX Titan GPU

Towards an understanding of teacher judgement in the context of social moderation

Social moderation involves teachers gathering together to discuss their judgements of the quality of student work and to reach agreement regarding the standard awarded. This qualitative study conducted over a three-year period investigated the social practice of moderation and the influence on teachers’ judgements of students work. An initial survey of teachers’ understandings of moderation and standards, pre-interviews of teachers who participated in the moderation meetings, observations of these meetings with a particular focus on one teacher (focus teachers) comprised the data collection methods. Data analysis involved organising, matching, coding, identifying patterns and themes using a constant comparative method. Socio-cultural theories of learning and assessment underpinned the approach to data analysis and proved helpful in explaining the diverse influences on teachers’ judgements beyond the task criteria, and the progressive development of shared understandings through engaging in professional discussions of students’ work. The study revealed that the process is not clear and linear and is influenced by factors such as the representation of the standards and the knowledge base of the teachers