Installing the Biobakery on Mac

Motivation This is a post written for students of BISC314 at Wellesley, but may be relevant for anyone else attempting to install the biobakery on a Mac. As of this writing, the homebrew recipes for installing several of the modules aren’t actually working on mac, so read on for some other options. The biobakery is a suite of microbiome and metagenomics analysis tools developed by the Huttenhower lab at Harvard School of Public Health.

Recursing the Seven Dwarves

I recently stumbled onto “The Riddler” series from Five Thirty Eight. Each week, they present a puzzle to solve that involves math and probability, and since I don’t already have enough to do :grimmace:, I thought I’d give this week’s a shot: Where Will The Seven Dwarfs Sleep Tonight? Each of the seven dwarfs sleeps in his own bed in a shared dormitory. Every night, they retire to bed one at a time, always in the same sequential order, with the youngest dwarf retiring first and the oldest retiring last.

Matching Publications to PubMed IDs

Earlier this week, I got an e-mail from Lucia Santamaria from the “Gender Gap in Science” project from the International Council for Science. They are trying to systematically measure the gender gap in a number of ways, including looking at publication records. One of the important parts of their effort is to find ways to validate methods of gender assignment or inference. Lucia was writing about some data found in the paper I wrote with with Melanie Stefan about women in computational biology.


A julia package for working with microbiome and microbial community data.

Kaggle Titanic Analysis in Julia - Decision Trees

Practicing using julia for ML analysis - taking inspiration from Ajinkya Kale Test and training data downloaded from kaggle and put into data/ folder. Let’s read it into julia: using DataFrames train = readtable("data/train.csv") tst = readtable("data/test.csv") describe(train) PassengerId Min 1.0 1st Qu. 223.5 Median 446.0 Mean 446.0 3rd Qu. 668.5 Max 891.0 NAs 0 NA% 0.0% Survived Min 0.0 1st Qu. 0.0 Median 0.0 Mean 0.3838383838383838 3rd Qu.