Resources for pivoting to public health data science

About two years into my PhD, I realized that the field I actually wanted to be in was public health, not necessarily biological engineering. Around the same time, I also fell in love with coding and data science. That’s when I realized that combining public health and data science could be an ideal career path for my technical abilities and interests and my desire to have social impact. But immersed in the world of academia, at an institution without a school of public health, and with mentors who had all chosen routes in biotech or academia, it was really hard to learn more about my options for pivoting to a career in public health. ... Read more


Racism as a public health crisis: how wastewater epidemiology fits in

Today is the Strike for Black Lives and a day to #ShutDownSTEM. For white people like me, today is about recognizing and reflecting on the anti-Black racism in our society, and committing to specific actions toward ending white supremacy. One of my actions for today is to publicly reflect on how our work at Biobot Analytics contributes to addressing – and potentially perpetuating – racism in public health. ... Read more

Mapping my cross-country road trip with Python

When I was on my cross-country road trip last year, I kept track of a lot of things in the hopes of doing amazing analyses when I got back. Turns out having a job as a data scientist makes it a lot harder to find time to do data science on the side, and so I’ve only really gotten a chance to look into my expenses. One of the things I had really wanted to do was make a map of all the places I went, but I didn’t actually know how to work with geospatial data in Python yet. I had this grand idea that I’d learn spatial data techniques while on my trip, but turns out hiking, drinking beer while watching the sunset, and going to bed early were way more compelling ways to spend my time. Luckily for me, one of the most fun parts of my new job has been learning geospatial coding and plotting techniques. I’ve been having fun with it in my job, and I realized that it also means I get to finally make my map! ... Read more

A Well-Kept Secret for Finding a Job post-PhD

During my PhD, I performed a lot of exit interviews with graduating students and learned that finding a job is often the most stressful part of graduating, and among the most stressful in the entire PhD. After my own defense, however, I was able to avoid some of that stress by discovering a valuable post-PhD job option that I had rarely heard discussed: getting a part-time or consulting gig after graduating to hold you over while you figure out your next full-time non-academic career move. ... Read more


Ultimate frisbee as a tool for social change

This is a guest post for 99 Days of Ultimate, a conversation held over 99 days that provides a platform for people to speak about a range of womxn’s experiences in ultimate frisbee. My friend Carolyn is this week’s moderator, and as an American living (and playing) in Scotland, she wanted to profile some of the differences between playing ultimate in the US and abroad. I spent a year in Cambodia before moving to Boston, which is also when I started playing frisbee more seriously. Part of the reason I became so passionate about frisbee that year is that I saw firsthand frisbee’s power to affect local change, and specifically in the context of gender equity. After returning from Cambodia, I joined MIT’s women’s ultimate frisbee team as one of the few graduate students on the team. Playing and becoming friends with the undergrads solidified my belief in the power of frisbee to drive social change and push gender equity forward. ... Read more

Road trip expense analysis, part 1

On my road trip, I kept track of (almost) all the money I spent. I was already fairly surprised with some of my quick calculations about how little I ended up spending (just around $4000!), and I also wanted to dive a bit more into how much I spent, where, and on what. So here we go! ... Read more

Road trip summary statistics

I (obviously) kept track of my mileage and expenses on my road trip, and a more thorough analysis will follow. For now, here are some fun and quick stats. Let me know if you think of more I should look into! ... Read more

Road tripping tips

If you’ve been following along, you’ll know that I just completed a three-month road trip across the US and back (in two parts)! I had an amazing time and learned a lot about traveling across the US. Here are some notes and tips to keep in mind for future road trips! ... Read more

Road trip FOMO: pro-tips and bucket lists

A few times throughout my road trip, I was hit pretty hard with some FOMO. I realized that it was in large part because I was sad to be missing out on things in Boston, like so many friends’ defenses! Also, I was sad to not have enough time to do all the cool things I wanted to on my road trip. So I wrote them down! If you are taking a trip through any of these parts of the US soon, please know that I will be living vicariously through you. ... Read more

On solitude

I’ve been spending a lot of time alone on this road trip. Both on this trip and over the past few years, I’ve been thinking a lot about solitude, specifically with respect to not having a romantic partner. I’ve been surprised with what I’ve learned recently. In my mind, there’s four different flavors of being alone: ... Read more

Disparities in the aftermath of sexism

I’ve been listening to a great podcast called Unladylike on my hikes, which has me angry and reflective (as good feminist content should). I’ve also been recounting stories on the phone while driving, and I’m noticing some commonalities. In my experiences, big disparities in sexism have come not in the actual sexist events themselves, but in their remnants, the emotions and impact after-the-fact. ... Read more

Words to become tourist-fluent in a new language

When I was living in Cambodia, I did a lot of traveling around SE Asia. One of my favorite things to do was learn just enough of the language to become “tourist fluent,” which meant that I could get around on my own and even make a few jokes here and there. I’d forgotten to write down the basic vocab needed to get to this level, but when I was in Malaysia last month a lot of it came back to me. Here it is! ... Read more

Graduation frustration

Graduating from my PhD was an incredibly frustrating process. I’ve been complaining to my friends about it for a while, and have been meaning to write up what exactly was so infuriating about it. One of the trickiest aspects of this whole thing is that while I knew that the graduation process is stressful and frustrating, I had no idea what all the relevant moving parts were until I was in the middle of it. Hopefully this can help graduating students maneuver their process, and give student leaders some insight to advocate for improvements. ... Read more

Live-tweeting conferences and making tweetable talks

I’ve gotten into the habit of live-tweeting conferences that I attend, and I really like it in part because I find it to be the best way to take notes, really helpful in lowering barriers to meeting in person, and a great way to raise your profile even if you are a lowly PhD student. Coming fresh off a conference and now that I’ve gotten pretty good at live-tweeting conferences, I wanted to share a few thoughts on tweeting scientific talks. ... Read more

Co-first-author non-academic PhD work

While the focus of my PhD was my scientific research, I also grew significantly as a leader and person through the extracurriculars I did. And even though none of those things will show up in my google scholar, I’ve been proud to contribute as “co-first-author” to many initiatives. I want to share them here, both as a reminder to myself and so that they can survive somewhere on the internet even if things in my department change. ... Read more

Graduation criteria

In general, I’ve come to believe that writing down standards and expectations is an absolute necessary first step to making any improvements. It’s a basic tenet of conflict management: “what would it look like for you to succeed?” In my last year or so as a BE Ref, I really ramped down the amount of effort and labor I put in to improving the BE student experience. It became so apparent to me that our department’s lack of consensus of what it means to be a successful BE graduate student meant that anything we tried to do could just so easily lead to us running around in circles: how on earth do you expect a student group to improve the graduation process for students, if no one knows or is willing to describe what is even required for graduation? ... Read more

PhDChat - a computational PhD as an act of self-love

A few weeks ago, I got to give a really fun talk to my lab and friends. A postdoc asked me to present at our lab summit (which is like a day-long group meeting), and I said I didn’t want to talk about my science because I was going to have just defended! Instead, I decided to use the time to get on my soapbox and talk about some of the things I learned and approaches I took during my computational PhD. tl’dr - love yourself, treat the PhD as an act of radical self-love and you will reap the benefits. ... Read more


Academia doesn’t deserve my labor

A Medium post by Eugenia Zuroski linked from Twitter, titled “Holding Patterns: On Academic Knowledge and Labor”, in combination with a brunch conversation in which my friend encouraged me to write down what I’ve learned from my advocacy work, motivated me to write this post. I honestly don’t know what I’m hoping to accomplish here. Maybe some part of me hopes that the faculty I’ve worked with read this and are spurred out of their complacency. Maybe being yet another voice calling out academia’s hypocrisies will magically tip the scale and lead to massive introspection campaigns from elite institutions. Or maybe I just want to be heard, and I want other student leaders reading this to know they’re seen and heard. ... Read more

Editing right ylabels in seaborn FacetGrid plots

Today, I figured out an answer to a question that I didn’t find asked anywhere on the internet. In case someone else (or me) asks this question later, I wanted to write up my solution for reference. This post goes over how to access and manipulate the right y-axis labels on a seaborn FacetGrid plot which was made with margin_titles = True. ... Read more

Talk about my science

I had a tense week with the internet a few weeks ago. I posted a tweet calling out a conference I was invited to for only having male speakers: ... Read more

The 64 bus

This morning, my roommates and I were discussing our bus-taking strategies: it was around 9 am, and one of them was about to go catch the 64 bus going to Kendall/MIT whereas the other one was planning to wait for the next bus, which goes to University Park. This got us talking about which route was faster: the Kendall/MIT route, which gets you closer to campus but seems to take a longer route there, or University Park, which drops you off farther from campus but gets there more directly. I had actually meant to look into this question in my previous commute blog post, so felt this was a great opportunity to do so! ... Read more

Commuting from Allston

About a year ago, I moved from my lovely Beacon Hill apartment (300 yards from the subway) to a house full of my friends (a 20-25 minute walk from the nearest subway stop). I’m super happy in my new house (we have chickens!) and it was totally the right decision, but at the time my new commute felt daunting - and many of my friends told me I’d regret giving up the convenience of my amazing Beacon Hill location. So, I did what any aspiring data scientist would do and started gathering data to prove them wrong. (See a theme in my data collection posts yet? XD) ... Read more

Hinge online dating experiment

A couple of months ago, I was having dinner with a friend who was trying to convince me to start online dating - he’s a hopeless romantic, and perhaps the only person on this earth who genuinely enjoys it. I really dislike online dating for many reasons and we’d had this conversation many times before, so I wasn’t interested in his arguments. But as he was telling me about the new app he was using, an idea started to form… Because of the way the app is set up, I realized I could test one of my longtime hypotheses, and in the process get some much-needed validation for why online dating sucks and definitively win our debate about whether or not I should sign up. ... Read more

Gendered experiences at a male-dominated conference

Last week, I attended a workshop focused on developing software for a popular bioinformatics platform in my field, which is a space that is much more skewed toward men than I’m used to (as a bio*engineer, I’ve been mostly spared from situations with extreme gender imbalance). It was an interesting experience, and overall incredibly positive. However, we live in imperfect world and I had an interesting gendered experience that I want to reflect on here. ... Read more

A year in the work life of a computational PhD student

I started tracking the time I spend on various “work-related” activities near the beginning of my third year of grad school. When I started, I hadn’t yet discovered the magic of tidy data so I kept putting off analyzing the data. Now that it’s been over a year since I converted to tidy data, it’s time to dig in and see how I really use my time! ... Read more

Developing a qiime2 plugin for non-developers

As a side project from the meta-analysis, we developed a method to correct for batch effects in microbiome case-control studies. When we posted the preprint on biorxiv, Greg Caporaso emailed Sean and asked him if he’d like to put our method into qiime2. I happily volunteered - I’d heard a presentation about qiime2 and was super pumped about their plugin setup, where anyone can incorporate their method into qiime’s suite of tools, and I was excited to see how doable it was. The learning curve was a little steep at first, but not as bad as I expected! Here, I’ve cleaned up my notes into a guide through my development process. I hope this is helpful to others like me, who aren’t trained computer scientists/developers, but who are keen and able to learn the programming stuff to make their tools more useful to more people. ... Read more

Slopegraphs in python

Slopegraphs are always introduced as being introduced by this Edward Tufte post, though this page is my top Google hit for “slopegraph.” I’m not sure if the kind of plot I’m talking about is technically a slopegraph, but in my academic circles that’s usually the term we end up settling on after a conversation that almost always sounds like, “you know, those plots which are kind of like boxplots except the paired points are connected with lines.” ... Read more

Blogging with jupyter notebooks and jekyll

One of the last parts before my full-fledged transition to github pages from wordpress was figuring out how to post nicely formatted jupyter notebooks. This was actually the reason I wanted to switch in the first place, but it turns out it wasn’t as straightforward as I’d hoped! I think I’ve found an acceptable, though imperfect, way to do this: here’s the general process I’ve settled on. ... Read more

Hitting the diversity wall

Some reactions to a recent Insider Higher Ed article on “Hitting the [Diversity] Wall”. The tl;dr of my thoughts: (1) Yep, the wall is real. Finding other students working to remind ourselves that we’re not alone in this fight is critical. (2) The fight is for transformation beyond “diversity and inclusion” - it’s about transformation of power structures. That’s what makes it hard and inspiring. (3) The strategies we take are important: when do we work with our departments and when do we demand change? ... Read more

Sharing AWS data with collaborators

I’ve recently become our lab’s AWS sysadmin, and my first task is to give our collaborators access to some of our data. In this post, I’ll briefly go over how I set that up and explain the different options that our collaborator has to access the data. ... Read more


Quotas work

In conversations about improving diversity in STEM, I tend to run into “well-meaning” faculty who are resolutely against quotas for fear that they will only exacerbate impostor syndrome and other negative perceptions (e.g. “you only got in because you’re black”). This is such a frustrating position and although I haven’t quite found a time, place, or way to push back against it yet, in my deepest heart of hearts I know it’s fundamentally foolish. ... Read more

Grappling with culture

I really struggle to form a response to this article, and to this line of criticism in general. I heartily recommend my liberal (privileged, sheltered, safe, and well-fed) friends to read this and grapple with it at least a little. ... Read more

Scatter plotting in python

In the past year or so, I’ve become a full-fledged tidy data convert. I use pandas and seaborn for almost everything that I do, and any time I figure out a new cool groupby trick I feel like I’ve PhD-leveled up. ... Read more

Professor superlatives

Our department is hosting an event called “Profscars” (like the Oscars, but for profs). The social chairs organizing this event emailed our entire student body asking for nominations for superlatives for each professor. A friend of mine pointed out that basically all of the women got superlatives based on their clothes/looks or mom status. I took a closer look and felt similarly appalled/taken aback, and then I did what any aspiring data scientist would do and decided to do some stats. ... Read more

Replication non-crises in science

I came across this great blog post again today while doing some literature search for one of my projects. I remember really enjoying this post when I first encountered it, and it was as much of a joy to read the second time around! What I appreciate about this article is that it doesn’t try to refute the contentious claim that “most [biomedical] research findings are false” but instead puts a “yes and…” spin on it. ... Read more

“Bad luck” cancer

Two years ago, a paper published in Science caused a big ruckus in the field when it argued that “the majority [of cancer risk] is due to “bad luck,” that is, random mutations arising during DNA replication in normal, noncancerous stem cells.” ... Read more

Thinx again

Saw this on my Facebook today, which links to this longer article about turmoil at Thinx. Some comments: ... Read more

Reflecting mansplaining

Active listening is a hallmark of conflict management. One of the most important parts of active listening is reflecting, which means that you basically say what the other person just said. Sometimes you can also reframe what they said to a positive, future-focused message (e.g. reframing a complaint into what they would want to be the case). Reframing is actually quite difficult to sustain, but reflecting is really easy - and transformative! ... Read more

Women in Data Science Conference 2016

Yesterday, I attended the Women in Data Science Conference in Cambridge. I went in hoping to learn more about data science as a field, to identify career opportunities in data science for computational biologists interested in public impact, and to feel inspired by being in a room full of women doing science. I’d say the conference wasn’t well-structured enough (i.e. tied together by a common theme) for the first goal and not varied enough in topics for the second one. That third goal, though - nailed it. ... Read more


The problem isn’t fake news

After the realization that I live in an echo chamber with opaque blue walls, I started following Breitbart news on Facebook. It’s been tough and enlightening, to say the least. ... Read more

Human-centered data

I just read two articles from my DataScienceWeekly email (so good! You should subscribe!) which do a really good job of humanizing data, talking so respectfully about its potential downfalls while also recognizing its tremendous opportunities for impact. ... Read more

Impostor syndrome

My thesis proposal is on Tuesday, which of course means that I’ve been thinking a lot about impostor syndrome. The way I process difficult emotions is by talking about them to my friends, and in this process it’s crystallized to me that impostor syndrome comes in so many different flavors, some of which are much harder to address than others. ... Read more

Seems like a good idea at the time…

Two older graduate students in my department who I admire quite a bit have personal blogs, where they post life musings, computational insights, and other thoughts on grad school. They also happen to be two of the graduate students with whom I’ve had the most pleasure working, students whose work and approaches jive very closely with mine, and who seem to “get” that the non-science parts of science are super important too. They’re probably going to graduate soon, so I figure I better start putting into practice some of the things I’ve learned from them. ... Read more

Ground Rules

When I was involved in CQA at Columbia, I learned that snaps are a great way to show agreement without being disruptive, and that Ground Rules are a wonderful thing to establish before having any sort of conversation. Ground Rules are about respecting the space, its occupants, and the discussion taking place. They’re meant to get everyone on the same page before getting into it the thick of it. So let’s get on the same page. Some of these are for me, and some of these are for you. ... Read more