Estimated reading time 13 mins (2576 words)
I’ve just come back from my second and last bioinformatics workshop of the summer!
From last Wednesday to Friday I spent 3 days in a row staring at a computer for 8-9 hours.
You might be thinking “Well, isn’t this what you usually do?”
Touché. It is.
But this time it was special because instead of spending 99% of that time googling problems and getting distracted/giving up on my Ph.D., I was learning a bunch of incredibly useful and time-saving skills at the 2018 Applied Genomics in Anthropological Research (AGAR) workshop organized by the American Association of Anthropological Genetics (AAAG). Look, academics just love an acronym…
Since these workshops are still all fresh in my mind, I decided to write a little post about them to summarize why I think doing workshops is a really good way of learning important material for grad students.
There are many types of workshops. Some are a few hours, others are a few days. They might be offered at your university or at a conference, or they might be independent events that you have to travel to (as was the case for me this summer). What they tend to have in common is that they usually draw participants and instructors from various universities (or various departments/ cohorts in the case of within-university workshops) and they tend to be given within a limited period of time (a few hours or days).
The combination of bringing together diverse groups of people and stuffing a lot into a short time period means that they are essentially the polar opposite of the kind of learning you do within a coursework situation. So, here’s my list of 4 reasons why I think workshops > coursework.
1. They are up to date
Many of the workshops I have attended focus on some technology/software that has only been used (or become popular) relatively recently. For example, at the AGAR bioinformatics workshop, Dr. Ellen Quillen and Dr. Genevieve Housman taught us how to manage/manipulate datasets in R and how to make amazing plots using various packages in the Tidyverse (honestly, the least painful R learning experience I’ve ever had, I’d even go so far as to say it’s the least painful stats experience I’ve ever had).
Though R has been used as a programming language and statistical software for about 25 years, it’s really only recently become the preferred program for any kind of statistical analysis. Mostly because it’s super powerful (anything you wanna do, you *can* do in R) and it’s open-source + free/gratis/no-cost/aka affordable for grad students. Statistical packages like IBM’s SPSS used to be more popular not that long ago. In fact, I was taught all my stats skills in undergrad on SPSS in 2013-2014. Yes, as someone who didn’t have coding skills, I was attached to the point-and-click interface. But lemme tell you what I’m not attached to – THE $99.99 PER MONTH MINIMUM PRICE TAG. There are few things I will spend 20% of my rent money on and a stats package is most definitely not one of them.
But to get back to the point. A lot of workshops teach skills that have only relatively recently become important/useful. Since R has a steep learning curve (relative to point-and-click software), many late-career faculty have gotten away with using what they are familiar with (e.g. SPSS). This is not ideal for grad students who are moving into a field which is expecting them to use the latest and best in order to be competitive.
In my department, we’ve had student-led and student-organized workshops on how to use Adobe Illustrator and InDesign because using MS Paint for image-editing and MS PowerPoint for poster designs just wasn’t cutting it anymore.
The point is that the content of workshops tends to be driven by necessity/demand of subjects and skills that may not be covered in coursework syllabi that have been recycled for the last 20 years. Since workshops usually invite experts on a topic, you’re not at the mercy of learning whatever your designated lecturer is willing to/capable of teaching you.
2. They are relevant to you
The great thing about workshops is that they are voluntary. So if you don’t wanna be there, you don’t have to! Coursework, on the other hand, tends to be mandatory.
There’s nothing I hate more than jumping through unnecessary hoops. But that’s the nature of grad school. In the U.S. at least. The U.K. system gives you a lot more freedom because it’s structure is simply “You’re in for a Ph.D. now, see you in three years – good luck!” (but that’s for a separate blog post).
All the coursework I’ve ever done has been because in order to get X degree I needed to check these boxes. And in order to check those boxes, it meant I had to go to X number of classes get a minimum of X on each exam do X number of homework assignments/essays etc. However, when it comes to workshops, the only reason I’ve ever attended a workshop is that I truly wanted or needed to learn something.
When I went to UW for the SISG, the reason I chose the module on genome-wide association studies (GWAS) was that this semester I’ve been struggling with figuring how to do GWAS and other types of association studies in R and with Plink.
Sometimes, you learn stuff that you didn’t even know would be useful. For example, I knew that I needed to process VCF files (a format used for genetic data) but I never expected that Dr. Maria Nieves-Colón would teach me how to do in 2 lines of code, something I had been struggling to do in MS Excel for 30 mins – 1 hour at a time. And don’t even get me started on how much time I know I’ve wasted based on what Dr. Ellen Quillen taught us to do in R. See for reference this tweet about my struggle:
The reason this point is not entitled “They are relevant. Period.” is that coursework is a mixed bag. Especially for grad students. If you’re working towards your master’s thesis or Ph.D. dissertation, you likely need a specific set of skills to answer the questions you’re interested in. This is not to say that having a broad knowledge base is a bad idea, but when you’re spending more time on things that are irrelevant to your final goal, that gets irritating and even stressful.
Grad school, and, in fact, your entire academic career, is about prioritizing. You’ll never be able to learn everything, no matter how much your sweet, nerdy little heart would like to. So, workshops are a great way of strategically learning those specific things you need to know in order to accomplish your goal.
3. They are concise and focused
When I arrived at Penn State I was introduced to the concept of “Sylly Week”. Sylly week is short for Syllabus Week. This is the first week of the semester where students are essentially just introduced to the syllabus and they have no tests, no homework, no quizzes, no work. Nada, zilch, zero things. And please do look it up, if you don’t believe me (it really is a thing).
While that might sound fantastic because it lets you ease into the semester, right?
HOWEVER, Penn State’s semester starts in August(?!???!) and it is SIXTEEN WEEKS LONG.
I’m sure some of you will not be shocked by that. But lemme tell ya, coming from Cambridge’s (three) 8-week terms to Penn State’s (two) 16-week terms was not an easy adjustment. I just don’t have that kind of stamina…
But the point I want to make here is that with that with 16 weeks to fill, I have seen some lecturer’s do funny things to plump up the syllabus. Sylly week is one of them, but then there are numerous “activities” that don’t always seem 100% necessary, like watching videos, quizzes for the sake of doing something, group projects that *must* be done during class time, presentations of papers etc. This is not to say that these activities are never useful teaching tools. It’s just that I have definitely seen them implemented in times that a lecturer a) didn’t have the time to teach/design a class, b) couldn’t possibly cram more material into the students’ brains, or c) simply had to come up with something for the students to do 16-weeks in a row, because they were expected to.
What I love about workshops is that you don’t have the time for useless fillers.
In fact, you don’t have time to do everything you actually need to do to learn how to do x, y or z. That’s why there is no fluff and no one goes on tangents.
A workshop is essentially a crash course and I LOVE me a crash course.
So after this completely unironic tangent on Crash Course, back to why being short and concise is great…
Most coursework I’ve taken has involved activities that probably were unnecessary, but were incorporated simply because you have to do something to fill the time. But, ironically, you take multiple classes at once and sometimes you can’t even find the time to do every assignment for every class.
Workshops are really short and intense. You focus on one thing at a time and then you can decide how to apply the knowledge to things you need to do. Personally, I think that’s the best way to learn.
4. Those teaching them and attending them are highly motivated – it’s a great place to meet people!
I’m sure we’ve all experienced this at some point in our academic careers:
The instructor doesn’t wanna be there. You don’t wanna be there. The instructor doesn’t wanna read your stuff. You don’t wanna write anything. Yet, here you both are, dealing with a 20-page essay nobody wanted in the first place. ¯\_(ツ)_/¯
Workshops usually don’t evaluate your work because there’s no time and you’re all there voluntarily. But the great thing is, rather than use grades as a carrot/stick approach to getting people to do well, you can assume that they wouldn’t be there if they didn’t want to learn.
One unexpectedly fun side effect of going to workshops this summer has been meeting a lot of amazing people.
It’s a great opportunity to broaden your horizons, however cheesy that might sound.
As an anthropologist, I barely think about non-primates let alone plants (soz, guys, it’s just not on my to-do list). But when I went to UW, I met a ton of plant geneticists. Not only were these really fascinating people, their research also allowed me to think about genetics in another way. Academic cross-pollination is a great thing (see what I did there? Cross-pollination, because they work with plants? I’ve really outdone myself here).
Also, there are only so many people you’re going to meet in your department and even within your university. On top of that, you’ll likely want to move on from wherever you are at some point. And if the first time you visit new universities or meet potential collaborators/colleagues is when you interview, that isn’t ideal.
When I went to AGAR in Buffalo, I got to talk with a lot of students who were struggling with the same issues as me (e.g. using R/RStudio, getting enough sleep, finishing their Ph.D., the usual…).
As someone who works in what is essentially a 1-person lab, it was really nice being around other people who shared similar research interests – first time in a long time I didn’t feel so lonely doing my work! (I swear this is not a cry for help, even though this totally reads that way, lol. But feel free to send some virtual hugs my way, those are always welcome).
But what I enjoyed most was learning from all these brilliant early career researchers. So many of the modules were taught by people who I genuinely consider to be superstars and getting to talk to them at the social events was super cool! It’s honestly so encouraging to find that people you admire are real human beings made of flesh and blood instead of these academic demi-gods who are better than you could ever aspire to be (who’s insecure? Me? What? Never).
Speaking of which, this particular group of instructors was hella funny.
On the last day, when we were taking group photos, we realized that three of them in the front were wearing the same uniform: plaid shirt + jeans. It was decided that they would make a fantastic boy band.
So, I introduce you to the new pop grunge sensation: PLAID JEANOMICS!
I designed the cover for their latest album:
Here’s everyone’s role, in case you were wondering:
If you want to learn about their research (the music is just a side gig), you can find more about them and their work with these links (from left to right, top to bottom):
- Onta Lin, Ph.D. – her lab page and some of her papers. She’s a Ph.D. candidate in the Gokcumen Lab at University at Buffalo.
- Joanna Malukiewicz, Ph.D. – her Twitter, WordPress, and GitHub. She is an affiliated researcher at the Federal University of Vale do São Franscisco in Brazil and incoming postdoctoral Marie Curie fellow at the German Primate Center, Germany and Instituto Adolfo Lutz in Brazil.
- Ellen Quillen, Ph.D. – her Twitter, lab website, and Google Scholar page. She’s an assistant professor at Wake Forest School of Medicine.
- Genevieve Housman, Ph.D. – her Twitter and website. She’s a postdoc in the Section of Genetic Medicine at the University of Chicago.
- Chris Clukay, M.A. – his lab page and his Research Gate profile. He’s an NSF GRFP fellow and a Ph.D. candidate in the Mulligan lab at the University of Florida.
- Maria Nieves-Colón, Ph.D. – her Twitter, website, GitHub, and Google Scholar page. She is an NSF Postdoctoral Fellow and a postdoc in both the Stone Lab at Arizona State University and the Moreno-Estrada Lab at LANGEBIO-CINVESTAV in Mexico.
- R. Antonio Herrera, Ph.D. – his Google Scholar page. He is a postdoc at Stony Brook University.
- Tim Webster, Ph.D. – his Twitter, website, GitHub, and Google Scholar page. He is currently a postdoc at Arizona State University and will be starting as an assistant professor of Anthropology at the University of Utah in January of 2019.
- Krishna Veeramah, Ph.D. – his lab website and Google Scholar page. He is an assistant professor in the Department of Ecology & Evolution at Stony Brook University.
- Omer Gokcumen, Ph.D. – his Twitter, lab website, and Google Scholar page. He is an assistant professor of Biology at University at Buffalo.
So now that we know what I choose to do with my free time, let’s just conclude this post.
Have you guys ever done workshops? If so, what do you think of them? Do you agree with me or are you less of a fan? Let me know, I’m curious!