PathoSPOT, an open-source bioinformatics pipeline that turns pathogen genome sequences sampled from patients into interactive visualizations of probable transmission scenarios. This is a public release of code originally written for my PhD thesis, described under the working name “PathogenDB” in chapter 4. To date it’s spawned two published outbreak investigations:

  • An under-the-radar outbreak of MRSA affecting 16 patients and spreading over 5 hospital wards, published (open access) in Genome Medicine, where the software is described in detail.
  • An outbreak of influenza A that started in an emergency department and involved 43 healthcare workers, 17 inpatients, and 6 other individuals, published in Clinical Infectious Diseases.

The East Harlem Software Company, a company that I cofounded with three other MDs (we all met through EHHOP at Mount Sinai): Kevin Hu, Ammar Siddiqui, and Mark Finkelstein. We design and host mobile-friendly web applications that support teams of physicians, medical students, and other healthcare workers, focusing on the rapid sharing of protocols, clinical guidelines, contact information, and other logistical knowledge that caregivers need at the point of care. An example of our work is the MGH White Book App, built for the Mass General Department of Medicine, pictured below.

Past work

  •, a website that displays random flashcards from the terrifyingly large Anki decks I’ve built over the first two years of medical school. The source for the web interface and Anki plugin is freely available.
  • ChromoZoom, a flexible, fluid, web-based genome browser built on HTML5, jQuery UI, Ruby, and a little C that I wrote while working for the Roth laboratory in 2012. The source is freely available, licensed as AGPL for non-commercial use. It was also published in Bioinformatics.
  • tqdm-ruby, which allows you to add a progress bar to your loops in the Ruby language. Great for terminal output while processing lots of things, or running a slow calculation within the cell of a Jupyter notebook.
  • jupyter-dark-theme, which themes your Jupyter notebook in dark tones so that you can hackety-hack on your data long into the night.
  • Dakota, a lightweight Active Record implementation for PHP5 built on top of Idiorm. Unfortunately I don’t use a whole lot of PHP any more, but this was the best I could come up with for getting data into and out of databases. The API was based on Kohana’s ORM library.
  • QuickFuse, a website that lets you build, share, and deploy interactive voice applications (a polite term for phone robots). Instead of writing code, you draw a diagram in a web interface that guides the actual callflow. Give it a try, you can seriously have a basic app running in minutes. I built this in PHP on the Kohana framework and jQuery UI while working for Plum Voice.
  • MedicaSafe, a medical device startup that aimed to generate data on prescription compliance using smart dispensers and present it to physicians.
  • Chillax was an experiment with jQuery UI and Web SQL that I made as a final project for a popular CS course at Harvard (requires Chrome or Safari). The source is on GitHub. The idea was to make an infinitely scrolling stream of stories based on RSS feeds that you choose, but for better or worse, I now use Tweetdeck and Twitterfeed for this, since Twitter is the new RSS.