stuff I've worked on

Open science

Organisations

  • I am a Mozilla Fellow for Science
  • Solvers.io (now retired), a place where programmers donate their skills to science projects in need of help. Co-founder with Dave Clayton.
  • ContentMine (also on Github), a Shuttleworth Foundation funded project in which we are building the technology to mine the entire academic literature as it is published every day, and republish un-copyrightable facts to liberate knowledge for all.
  • BioJulia. A community building bioinformatics tooling for Julia, and holding itself to the highest standards in its work and culture.

Software

  • getpapers, the easiest way to download hundreds, thousands or tens of thousands of scientific articles at once.
  • scraperJSON, a schema for defining reusable web scrapers as JSON objects.
  • thresher, a scraperJSON web scraping library for Node.js.
  • quickscrape, a command-line tool for scraperJSON web scraping that uses thresher as a backend.

Learning

  • Command-line bootcamp. Learn the UNIX command-line by following an interactive adventure in your browser.
  • AnkiMobile, the iOS version of the world's best flashcard app, Anki. This consumed me for most of 2012 (and funded my undergrad).

Computational biology

These are all works in progress...

General academia