About a week ago, I had the opportunity to participate in an intensive, two-week long workshop offered by the Data Intensive Biology Summer Institute (DIBSI) at UC Davis that taught me how to analyze genomic and transcriptomic data sets, which tend to be very large (in terms of computer storage units, these data sets are often multiple gigabytes or sometimes even entire terabytes in size) and hard to handle. With recent breakthroughs in sequencing technologies that are making it easier and cheaper every year to read your favorite organism’s entire genetic code base pair-by-base pair, I think we can truly say that we’re living in the golden age of biology. And while this means that we can now begin answering the deepest questions about how life on earth evolved or discovering ways to alter genetic sequences to improve the welfare of our species and those that share the planet with us, the simple truth is that with all this power, we’re capable of collecting more data than we sometimes really know what to do with.
Therein lies the power in ANGUS and other workshops like it (check out Data Carpentryfor more info). These workshops take researchers that have big, bold, beautiful dreams about how we can utilize these often overwhelmingly large genomic datasets to understand our world in new, intriguing ways, and gives them everything they need to be successful in their scientific pursuits. But more than that, they teach the participants how to avoid major pitfalls and frustrations that often discourage scientists from exploring the genomes of their research organisms in the first place.
In short, the trainers at these workshops are miracle workers.
But before I tell you in full where the workshop has taken me, I’ll tell you first where I began.
Before I started ANGUS, I was terrified of coding and the command line. Trying to do even simple tasks using Terminal or R brought me serious anxiety, and in my graduate coursework, I never felt the Imposter Syndrome as strongly as I did when we had to complete assignments in R…I felt as if all my classmates sailed through the assignments while I puttered slowly along, getting more and more discouraged with each little error in syntax. Honestly and embarrassingly, I thought it was something only “smart” people did (even as I write that now, I feel foolish). Worse still, in my head, I had this incorrect picture from popular media about who a coder was and what a coder looked like (usually male, usually white, usually an ace at all things mathematical, precise, and rigid), and I never thought I fit that bill in any way. I revel in subtleties, in the qualitative, in description, in prose. And I felt like coding could never be something I could be interested in, let alone be any good at.
But on my last day of ANGUS, when I looked around at all the diverse faces in the lecture hall, at all the women, the men, and the gender non-conforming, at the students from Italy, the UK, Japan, Kenya, Brazil, and all over the US, what struck me most was that, after our experiences at the workshop, we were all coders. We could all do it. I realized then that anyone can do it, and that was ANGUS’s biggest gift to me. Well, that…and the pages and pages of notes, all of the know-how, a Rolodex chock-full of high-powered, helpful, friendly bioinformaticians, and a ton of usable, operational, clearly notated scripts and lines of code…but the huge boost in coding confidence was a definite plus!
Now when I sit down to bioinformatically examine data, I feel excited and confident, driven to identify patterns in the data that further pull back the veil of the biologically unknown. Every successful line I run gives me affirmation. And even when I run into errors, instead of shutting down in a cold sweat, the part of my brain that loves to solve problems lights up, and I use the resources I learned at the workshop to debug my code.
How incredible a thing is that? ANGUS took me from zero to bioinformatic hero in two-weeks time. If that’s not a miracle, then I don’t know what is.
Resources
If you’re interested in working on improving your own proficiency with analyzing high-throughput data, all of our lessons from this year are freely and publicly available online! Why not give it a try?
-Victoria
P.S. If you’re working through the ANGUS lessons and you run into trouble, shoot me a message with your error codes and we can debug them together! 🙂
P.P.S. Go tigers, go!!! (Note: the adorable featured photo is in reference to the three training rooms used at the workshop: Room Lions, Room Tigers, and Room Bears (oh my!))
P.P.P.S.
As he noted, our world is indeed beautiful and elaborate and complex and diverse. He took his inspiration from looking at a riverbank bustling with life, but all we need to do is slow down and take a closer, curious look at any living thing around us. I’m a marine biologist by training, and every time I dip my head underwater, I find my breath catching in my throat at the stunning grandeur of life. It truly is spectacular.
🦀 origami crab 🏝️ 