Perhaps it would be wise at this juncture in the course to take a pause…
Friday ensued with two lectures and much eating, drinking and dancing merriment! I was admittedly totally lame and went home early to sleep as I was falling asleep at the Music Bar table despite the excitement around me. I did however witness the B52 flaming shots and that was a sight to behold prior to passing out wholeheartedly in my bed.
Perhaps tonight it was the 10+ tastings of wine from this evening at the Puppet Muzeum…perhaps it is the rather potent tea that I acquired at the tea room (cheers to Marie for suggesting the place to me!), perhaps it was the permeating smoke of grape flavoured hookah wafting around me…nonetheless, I got to thinking and ‘miserating with the position biology students are in today in terms of biology as a field moving toward the more computational.
I agree computational is a scary word at times, it implies math, statistics, programming–I imagine myself running screaming from the room sometimes. But really how is it any different from the statistics you are required to do for your research/Ph.D. anyway? Nothing changes essentially, just instead of designing a PCR assay you are designing a computerized sequence analysis pipeline (CSAP)? How is that for an acronym!? You learned best practices for designing a PCR assay and now you are learning some good practices for designing and implementing an NGS study. However, the details will always be up to you.
As a Ph.D. student or as a Post Doc you eventually, one day, will be considered the expert in your field and that requires knowledge of all aspects of a field that, admittedly, is now changing quite rapidly underneath you and toward the computational. One of the things we’d like you to draw from this workshop, right now, is in the field, there is ‘no right answer’; you try what is out there, you compare; and you draw your best scientific inferences from the information that is available to you…remember you are a detective! During your defense or during your funding review/application, how will you reply to the question?: “Gee, I noticed you used such and such parameters…why?” I guarantee you “Because so and so used them in his 2013 paper…” will not suffice. So start learning and working out your logic and justifications now. Everything in the field is suspect right now and so if you decide to use something, be prepared to defend it, to own it, to say I did this sh*t forwards, backwards and inside out and I STILL got this answer. And if you get different answers, don’t get frustrated…get intrigued and figure out why that happened or what perhaps to do next going forward.
Don’t know a unix command? ‘man’ it.
No ‘man’ for your unix command?…google a unix cheat sheet (Google is a glorious mistress! She always puts out and usually the good stuff pops up first assuming you chose the right keywords. Ok, I realize this is TOTALLY an inappropriate analogy…but really, it’s kind of true and if you’ve been reading this blog through you shouldn’t be surprised by my analogy.)
Don’t know what a particular flag means for a particular program…look it up in the documentation often by typing ‘program name’ -help or -h
Said program ‘man’ or help page is not installed or available? Google it (program name + sequencing or + assembly or whatever other specifier specific to the program, helps in specification)
Don’t know why you have no ‘out’ file? Look at the onscreen output…is there an Error in there? Look at the Log file, is there an error in there? Read the error try and track down where it is and how to fix it, many programs will tell you exactly what is wrong.
Still don’t understand the error/output, perhaps you got no output at all? Check your command, you’d be surprised how 1’s can look like I’s and spaces can be left out or included when they aren’t supposed to be. Did you put a dash instead of an underscore? Did you specify the right directories so the program could navigate to the right files? Did the program want a single dashed flag and you put double or vice a versa did it want a double dashed flag and you put single? Did you copy paste (ayah!) when you should’ve been typing? Some word/pdf docs don’t copy/paste well to the command line.
YOU are the master of computation, not the other way around…OWN it, WORK it, HATE it, LOVE it, LIVE it and on occasion…perhaps take in some very strong tea and breathe in some very thick hookah smoke to gain some perspective, however hazy, on your situation, go outside into the clear frosty Czech (Alaskan/American, Swedish, English…) air, take a deep breath and start again. If you are from Australia or Thailand…breathe in some hot humid air, go find some air conditioning…and start again.
Much luck to you all in the coming week; the instructors and faculty are here for you, definitely utilize the faculty while they are around!