Resources
PyBamView is a browser-based tool for visualizing next generation sequencing alignments from BAM files.
A list of useful IPython tools I've made/compiled from other people that I use in my IPython presentations.
A short talk I gave at the Fall 2013 Arvados Summit on the advantages of building tools like lobSTR on the Arvados platform.
Step-by-step instructions for getting started using Amazon Web Services with 1000 genomes data. Goes through setting up S3, EC2, and Elastic MapReduce.
The lobSTR tool takes in raw sequencing reads from next generation sequencing platforms, and outputs genotype calls at short tandem repeats. It is compatible with standard BAM and VCF formats.
PTMScout is a web application for viewing and analyzing data from mass spectrometry experiments and other datasets for post-translational protein modifications. The goal of PTMScout is to provide a useable interface for biologists to easily work with large datasets of post-translational measurements.
Lecture notes on fun game and puzzle related math topics. My classmate Jing Li and I created and co-taught this seminar at MIT at the ESG program from 2009-2011.