I’m passionate about open source software and a big fan of the Python scientific computing ecosystem and community. Below are some of the open source projects I’ve initiated and played a major part in developing.

  • malariagen_data - A Python package providing a cloud-native interface for accessing and interactively analysing genomic data from the Malaria Vector Genome Observatory.

  • zarr-python - a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing.

  • scikit-allel - a Python package for exploratory analysis of large scale genetic variation data.

  • pysamstats - a fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

  • petl - a general purpose Python package for extracting, transforming and loading tables of data. This was my first foray into open source software.