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Friday, June 6, 2008

Playing at work...

One of the fun things about doing science research is that you don't really know what the right answer is until you test a bunch of potential solutions and figure out which one (if any of them) is right. For the computer nerds and engineers out there, science research is really reverse engineering nature. Scientists come up with a theory, and then do their best to figure out whether they're right. I think that's one of the things that the non-scientifically inclined don't understand: We're constantly refining our theories to better incorporate the subtle nuances of how nature works. It's a game of trying to understand and really "grok" how the universe functions - which has always been one of my favorite pastimes.

Anyhow, where I was going with that is to talk a little about some of the work I've been doing lately, and why it doesn't seem like work.

I'm trying to split my time between three projects; developing new (and hopefully improved) methods and software for the analysis of ChIP-Seq experiments, developing new (and, again, hopefully improved) software for analysis of whole transcriptome shotgun Illumina sequencing software, and finally, trying to analyze the results of the whole transcriptome shotgun sequencing I'm supposed to be working on for my PhD work. Each project has it's own amusement value, and it's surprisingly different.

I spent the last 3 days hammering through the changes to my next version of the FindPeaks software I'm working on. It turned out that the development model I had in mind was completely impossible - which obviously slowed my progress down well beyond what I expected. (Apologies to my collaborators!) However, along the way, I tried several new things, which gave me a lot of opportunity to refine the application. The code runs faster, performs vastly more in depth analysis of the results, sheds light on several things we'd never observed before, and has the potential to change the way we interpret ChIP-Seq data. To a scientist, that's fun: the discovery of something unexpected.

With the transcriptome software work, I've only been working on it incidentally this week, so I have less progress to report. It represents more of the usual type of science... the grinding work that goes on behind the scenes. While I may not be excited about the work itself, I can look back over the past 6 months and see how far it's come. Maybe it's not "fun", exactly... but I can take pride in the progress. By next week, I'll be able to hand over a lot more code to my collaborators on this project.

The last project, the interpretation of my own data set, is something else entirely. It's not fun, and not really pride in work well done, but just the thrill of basic research. I'm not seeing anything unexpected - but I am seeing something new for the first time. Being the first to peel back the layers and see what's going on under the hood in a cancer cell line is pretty cool. I may not understand everything, but it's all new. I'm sure it's the same thrill, albeit somewhat less grand, of an explorer being the first to climb a mountain, visit some remote corner of the earth, or take the first step on the moon. The newness doesn't fade quickly.

Between the three projects, I definitely find that there's a lot of excitement and entertainment in the grad school experience. And, as my friend Abby reminded me today, if you're having fun doing something, it's not work.


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