A blog about it > NGS 2013

I know, there was a time before NGS 2013 when you probably thought that > was just an innocent greater than symbol. You didn't know what the hell to do with something like this | and in your mind "cd" was an outmoded flat disc that was once used to play music. And then... you met the power and the glory of the command line, which totally rocked your biological world. That is, when weren't hating on it for returning output like "putty, putty, putty" (repeat ad nauseam in weird computer voice). Then you took it to a whole new level with commands like "gunzip" and "tar" - the latter followed by those 4 alphabetical letters that no one ever remembers (xvzf?). You also quickly learned that it is going to be necessary to type at the command line with lightning speed, keeping the error rate down to about 1 typo every 100 words, at least for amateurs. And to think that this was all happening on day 1! Thanks Adina Chung Howe.

So what, pray tell, am I talking about? MSU NGS Summer Course 2013 is a two week course on next generation sequencing technologies that took place at the WK Kellogg Biological Station, a summer retreat built by the vaguely weird tycoon of Kellogg cereal fame. Why weird? Small fact communicated by Rachel Prunier, one of the NGS students: apparently said tycoon was fascinated by the anti-masturbatory properties of excessive consumption of raisin bran. Upon reflection, I can sort of buy into that.

Ah yes, where were we? NGS 2013! In short, the best experience ever. Learning and otherwise. We were a group of 24 (hard to put this in the past tense, the memories being so fresh) that came from all over geographically - a motley crew of PhD students, industry types, post-doc, professors, and even a stray masters student. We came to mecca primarily to learn about what to do with our BIG DATA. For those of you who are not well acquainted with the term BIG DATA, well trust me, it's big. In more ways than one. Moi, for example, has taken a venom duct from a marine snail and turned it into 289 million reads of raw sequence data, aka cDNA. Actually I came to the course with some assemblies as well, but no matter how you slice it, the DATA is BIG. The drill is, we dumb biologists (hah, Titus Brown, I said it!), don't always know so so well what to do with it once we have it. For this we rely on the more computationally advanced types, highly trained computer scientists, who probably could not work their way out of a wet paper bag in most situations, but who do excel when it comes to BIG DATA.

Unraveling, or perhaps re-raveling, this big data is in fact a hugely important challenge, if we want to get at the secrets of nature as encoded by genetic material spelled out by those four simple nucleotide bases - adenine, guanine, cytosine and thymine (uracil if you are counting RNA). Which in every case, for every student, is why we came to the course. We 24 lucky ones were selected from a pool of over 200 applicants. Jokes about challenged biologists aside, we were a group of pretty smart cookies, if a bit at sea when it came to bioinformatics. Participants were working on all sorts of organisms -- sea anemone, bacteria, human, equine, and so forth, each with their own assorted set of biological questions.

But wait, I am many paragraphs into this blog and I have not even explained C. TITUS BROWN. Boy, I bet he's a little ticked off. The fact of the matter is, he's a little hard to explain, but he is kind of awesome. When he's not being snarky and stubborn. Which is of course, not most of the time. C. Titus Brown is the founder and leader of NGS 2013, or the guy who got us to drink the big data and what are we going to do with it kool-aid. The course is now on its fourth year, though I suspect it has never seen a group quite equivalent to the likes of this year. Suffice to say we exceeded expectation on all fronts. Objective assessment, I promise.

So how did this course go structurally? Well we arose at the crack of dawn, more or less, and headed to the Carriage House for lectures, tutorials, and desperate pleas for help from the crack group of teaching assistants, who really came for the volleyball and the beer. Around 3 or 4 PM we would break for, you guessed it, volleyball! or frisbee or swimming in the lake. Or just a bit of lazing about. In the morning we learned about assembly programs, SAM, BEDTOOLS, BAM TO BED, BWA, Bowtie, TopHat, Cufflinks, you name it (all very useful), and in the evening (post physical recreation) various lectures on research (a couple of really astoundingly wonderful talks by Erich Schwarz, morning or evening) or other NGS topics of interest. I would also be totally remiss if I did not mention Istvan Albert, who has an unprecedented combination of razor sharp intellect and pure joie de vivre.

I could write a whole lot more about this. But for now, I will just leave you with the flavor. For me, and I suspect for a number of other participants and teachers as well, it was the experience of a lifetime. It was the perfect blend of rapid fire learning, intellectual stimulation, camraderie, sports, firepits, judicious amounts of alcohol (mostly), and great good fun. I would go back in a heartbeat. Ultimately, we delved far deeper into the world of bioinformatics and NGS than learning about basic linux commands, referenced in paragraph one, on day one. So yes, Titus Brown, next year, three weeks! For that final week, I think I can speak for most if not all of us, we are IN! :)