PROJECTS

• Hacker News Trending

  2018-09-24

  Hacker News is a great source of tech-news. However, the site has a very high turnover rate in terms of stories. If you do not check it daily it is easy to miss something.

  That is why I created Hacker News Trending (HN Trending). HN Trending was a simple website that aggregated Hacker news stories by popularity over the past week, month, year, and over all time. After 4 years I decided to shut down hacker news trending.

  • Hacker News Trending
  • Front page Hacker News Story
  

• IEX API Python

  2018-05-27

  IEX-API-Python is a python wrapper for the IEX API. IEX-API-Python can be used to retrieve financial data such as stock prices, news, or company information from IEX. Data can be obtained as JSON or converted into Pandas DataFrames.

  IEX is an exchange founded by Brad Katsuyama and written about in the book Flash Boys by Michael Lewis.

  • GitHub
  • Documentation
  

• Upvote.pub

  2018-02-01

  Upvote.pub (https://www.upvote.pub) was a shortlived experiment to create a reddit-style clone specifically for scientific publications. Users could submit scientific publications from arXiv, bioRxiv, PubMed, or using a DOI. These submissions could then be upvoted or discussed using a commenting function (which also featured upvotes). I created the site because I like HackerNews and reddit, and I believe more dialogue regarding scientific publications would be a great thing.

  The site made the front page of HackerNews and drew mixed criticims. There are some subreddits which provide similar functionality. I have open-sourced this project.

  • Github
  • Hacker News Submission
  • Screenshot 1 - Submission screen
  • Screenshot 2 - Story
  • Screenshot 3 - Subs config
  

• VCF-Kit

  2017-05-15

  Abstract

  The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit.

  VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools.

  • GitHub
  • Publication
  • Documentation
  

• elegansvariation.org

  2016-02-26

  The C. elegans Natural Diversity Resource (CeNDR) is scientific web application that enables users to perform genetic studies. The web application is deployed using Google Cloud Platform and is written using Flask, a python-based web framework.

  The site features a genome-browser, a catalog for ordering scientific specimens, a download portal, and can also launch analytical pipelines for performing analyses. CeNDR is actively used by the scientific community and has become a valuable tool for performing studies.

  I developed this resource during graduate school.

  • Github
  • CeNDR (elegansvariation.org)
  

• Open Source Contributions

  These are open-source projects that I have contributed to, but did not initiate.

  • mosdepth - [nim]; Helped develop summary stats of coverage data.
  • memoise - [R]; Developed cloud-based memoisation on aws.

• Mini-Projects

  I have also developed a few utilities / tools you may find useful.

  • Awesome-Bioinformatics - A list of awesome bioinformatics software.
  • gist-alfred - A workflow for searching gists in Alfred.
  • Quiver-alfred - A workflow for searching quiver notes in Alfred.