In this article, we report on our experiences with refactoring a spatial analysis library to support parallelization. Python Spatial Analysis Library (PySAL) is a library of spatial analytical functions written in the open-source language, Python. As part of a larger scale effort toward developing cyberinfrastructure of GIScience, we examine the particular case of choropleth map classification through alternative parallel implementations of the Fisher-Jenks optimal classification method using a multi-core, single desktop environment. The implementations rely on three different parallel Python libraries, PyOpenCL, Parallel Python, (PP) and Multiprocessing. Our results point to the dominance of the CPU-based Parallel Python and Multiprocessing implementations over the Graphical Processing Unit (GPU)-based PyOpenCL approach.

UNLABELLED: The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples. AVAILABILITY: http://www.sanger.ac.uk/genetics/CGP/Software/AutoCSA.