Friday, April 3, 2009

it was really cool to overload the Broad's servers, until it ended up that all my hard work meant absolutely nothing.

Some of you might have heard me excitedly smile today that I have overloaded the Broad's servers... (before I go on, it's pronounced Brode rhymes with road - I can't have you all thinking it's Brawd rhymes with cod, otherwise you'll make mistakes I have already made quite enough thankyouverymuch). It was a feat I considered pretty impressive (my brother told me I should put it on my resume) ---that is until I realize it meant that I had spent hours and hours and hours on this project for nothing.

I'm doing a grant proposal right now for a class which is analyzing microarray datasets (we're talking 22,000 partions of data corresponding to the entire genome). My goal is to find specific genes that are upregulated and downregulated when a specific drug stimulates cells using hierarchcial clustering (I don't get how it works, really. That's why computers do it). If you know a specific genetic footpring cause by a drug, you can sometimes figure out how the drug is actually working, or a better idea of other drugs that are similar to it for novel drug targets for your disease/condition of choice. I'm working on Hyper IgE, a confounding/odd/mostly unstudied disease where your body produces too many IgE molecules (IgE is a type of immunologlobulin: it's a specific antibody that works inside your body to deal with infection; it's now best known for being involved in allergic reactions). So this is cool...and it's interesting to me.

But there is a problem. These datasets are enormous. Huge. Gargantuan. I had to download all of these signatures from one website, convert them all into a different file type, and then run them through an online program run by the Broad. I was having all sorts of trouble until I finally broke down and emailed their support staff, a guy named Peter (yup--first name basis now). He said that my datasets were just too large for the main server, so he set me up in the queue for the larger memory servers (which will allow my data set to run, but since so many people use them and they are in such high demand, the samples will take a long time to run). I also found a bug in their viewing program, which took them quite awhile to fix. Ultimately (21 emails later), I was told that all the data sets I had were confirmed incomplete (the server simply gave up). Which means I am at square one.

I cannot tell you how frustrating it is to tell a professor that you have worked really hard...but you have nothing. It's so sad...I just turned in my preliminary data, and it contains a table that is all filled up...except for these awful white cells that pretty much scream FAIL. Sure, my specific aims are lovely, and I have a nice chart about the drugs I'm looking into, but the actual meat of the proposal is simply missing.

I realize I didn't start soon enough. I realize I know little to nothing about computational work. I realize my poor five year old computer is about to 'splode from all of this abuse. I realize that I should have expected more problems initially and contacted the Broad immediately. I realize that even though I have spent every waking moment in the past week on the project, I have absolutely nothing to show for it.

But I also realize that I have been working so hard this semester. Trying to juggle lab and classes is driving me nearly batty. I am always always ALWAYS behind in something. And for someone that is happy to breathe a sigh of relief at the end of a day feeling on top of things, this is just not okay for me. Sure, people tell me "it'll be over'll be fine." Sure, I'll be "fine." ...if your version of fine means that I'm operating in a completely unsustainable fasion and inch away from just giving up because there is simply not enough time to do everything.

I am so behind. And glad that I wear exclusively glasses these days--because my eyes betray how much sleep I am getting. (although you can't miss the slight hunchback from all of this computer work). Excuse me while I go and drown my sorrows in dirty dishes and chocolate.

Update: it's a new day (thanks mom!). And it's going to start with Bollywood. So there, life. Take that!

(from Kal Ho Naa Ho - sorry about the bad quality, but it's a great cover...)


M. said...

I firmly believe that Bollywood makes everything better.


Rick L said...

I have most definitely seen this Bollywood movie before. How did you get hooked on it?

Bridget said...

I had loved Bollywood music, but I didn't really have the chance to see any of the movies until last year - my roommates and I took advantage of one particular roommate's netflix account at the insistence that we HAD to see Kal Ho Naa Ho ---so we did. I loved it. The combination of color saturation, happy music, tears,