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.

Getting Back on the Horse - Part 2: Deploying a new Site

Yeah, so my last post was clearly a bit too optomistic. I’ve only just now set up this new website using the Hugo static site generator and Academic theme which is pretty nifty. I started doing this back in August, but ran into some snag and haven’t returned to it until now. But I thought I’d briefly go through what I did in order to set this up, mostly as a reference for myself.

Getting Back on the Horse

Well, it’s been far too long since I wrote anything here. In the mean time I’ve: completed the HMX biochemistry course Got two papers accepted (eLife paper on HGT is out, PLoS Comp Bio paper needs some final touches) started a postdoc in the Huttenhower lab and… that seems like enough Also finally updated the header image on this site to be one of mine rather than the default.

Diversity and Academic Freedom

I recently had reason to go and dig through some of my old blog posts at ScienceBlogs - in particular, this one on diversity and this other one on academic freedom vs bigotry. Though I often feel like I’ve gone through a rather major intellectual overhaul in the past couple of years, I’m happy to say that I can stand behind the stuff I wrote back in 2010 and 2013 on these topics.

What to trust

The Expanding Universe You may have heard that the universe is expanding. We can tell because the light from distant stars is redder than it should be. Like the sound waves of an ambulance siren as it speeds away from you, the waves of light from these stars speeding away from us are stretched. Longer sound waves are deeper, longer light waves are redder. It’s easy for me to believe that this is true, though I’ve never measured the wavelengths of light coming from a distant sun.

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.

The Limits of Privilege

Some musings about the most recent US presidential election.