Modular and universal bioinformatics

XIV Congress of the European Society for Evolutionary Biology

Github profile and CV

My website

Blazing fast Neovim framework providing solid defaults and a beautiful UI, enhancing your neovim experience.

Simple test Nextflow pipeline for testing GPU capabilities with cloud systems such as AWS Batch

A stampede of processes at your fingertips

A proof of concept RNA-Seq pipeline with Nextflow

Emacs mac port formulae for the Homebrew package manager

Custom Nix packages not yet available on NixOS/nixpkgs

GFF parser

Pixels Camp v4.0 (March 2020) call for talks — submissions

Streamable FASTA parser.

Node.js module for working with the NCBI API (aka e-utils).

📦 Stencila's Nix packages collection

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

🐳 A Docker image builder for researchers

Back-end of the Python 101 course for biologists

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

QMUL's programming in R course

A Web App for analysing GEO (Gene Expression) data

Nix Packages collection

Dockerfiles

The go-to place for materials, contributions and work for the 2016 Mozilla Fellows for Science.

Lightning Talks from the Mozilla Festival October 28-30, 2016

:bangbang: :page_facing_up: :mag: an API and web interface to check if a paper has been retracted

NPM module that wraps request to allow Stream of URLs as input

OBF Google Summer of Code

2017 MozFellows Workweek - SF

try bionode using docker

My Dockerfiles. Trusted Builds also available in the Docker registry

Transform stream for Node.js that allows you to run your transforms in parallel without changing the order

HTML to Reveal.js

A web wrapper for GeneValidator

Intuitive local web frontend for the BLAST bioinformatics tool

Spawn and expose docker containers over http and websockets

A simple Heroku app template for deploying Dat

real-time replication and versioning for large tabular data sets. pre-alpha!

Bionode Demo at CW15

Talk about the PSMC, given in the Evolution Group Lab Jolly at the Queen Mary, University of London.

Hiring a genomicist

Bionode demo for a wurmlab meeting

Random scripts repo (for when using gist isn't the best).

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

Small talk given at the outreach event for the Population Genetics Group 2015 meeting

Auto correct and generate reports for exams results stored in Dat

Proxy to access resources that lack the Access-Control-Allow-Origin * header

Node.js module for working with Streams of objects.

dockerfiles for nodeschool

MSc Bioinformatics - QA and Assembly

Talk for TGAC - AllBio 2014

Talk given at wurm lab meeting, before allbio14.

interactive nodeschool online

Fetch elife XML from AWS S3 into Dat

Node.js Stream interface for Amazon Web Services (AWS)

Stream interface for the Node.js module pace

Converts XML to JSON, using Streams and sax. This can be used with above-memory-limits XML files, as long as they're mostly composed of a repetitive tag.

Quickly figure out time in other timezones.

Genome Annotation for the Masses

misc code and scribbles from our hack days

Python 101 course administrative stuff

AngularJS app that uses many APIs. Used in the new CoBiG² website.

Python 101 course slides

Dockerfile for Trusted Build of the image with the Afra project dependencies

Lightning talk (5 min) given at the Citizen Cyberscience Summit 2014

Lightning talk (2 min) for the Collaborations Workshop 2014 at the Software Sustainability Institute

Talk given in a seminar at the Queen Mary, University of London.

My Archlinux PKGBUILDs files

Tools for bioinformatics

Stuff that I've made in inkscape, gimp, etc, for various purposes.