stuff I've worked on
- 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.
- 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.
- 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).
These are all works in progress…
- transrate (+ Github), a command-line tool and Ruby library for quality analysis of de-novo transcriptome assemblies.
- chain, a tool for taming bioinformatic pipelines.
- biopsy, a framework for optimising any bioinformatic software.
- assemblotron, fast, automated, optimal assembly of transcriptomes using any modern assembler.
- Tools for RNAseq, transcriptome assembly, and working with NGS data.
- hibberdlab.com, the website for the lab I’m in.