Thursday, November 14, 2013

Watch out below!!!!

*Image from goodle images


Ahhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh, that feels much better....................................................NOT!!!!

This is just where I am right now and how I'm feeling about my Bioinformatics course too!! Double URGH!!!!!

So here's the problem, after TWO WEEKS of trouble shooting, I FINALLY got a program given in class to work. Why did it take ME so long? They use the Mac operating system (OS), and I use Ubuntu. Why do I use Ubuntu when almost NONE of the folks at school doing this type of work use it? Because in the "real world" of Bioinformatics, most folks program in Linux which is what Ubuntu based on. And in a field like computer science, a LOT of what you learn in school is not only obsolete by the time you finish your program, you can be pretty sure that in the "real world", no one or few people are using what you learned in school.

That said, many people in Bioinformatics use the Mac OS (like the NIH), it's just that since most Bioinformatics departments are made of Computer Scientists (who have honestly mucked it up IMHO), you have to learn to use the OS they frequently use. And this creates a situation where from an employment point of view, they'll always be needed since it's just too much trouble for the average Medical/Life Scientists (MLS) to be trained to do this stuff. Along those same lines, it's also the reason I sense a tiny bit of resentment from a couple of the computer scientists (CS) folks I work with. But I digress, the point I'm making is that taking the leap from Medical/Life Science to essentially computer science is the MOST challenging thing I've EVER done. But personality wise, I'm so well suited for it because: 1) I'm as tenacious as they come and 2) I enjoy challenge of leaning something new. And like it or not, a LOT of medical science and research is going to involve a significant amount of computer generated data (human genome, anyone?) in the future. So yeah, my code may not be as "pretty" as that from a CS person, but it's functional. More than that, other people like me can understand it because I write it in a way for folks like me to understand.

Here's an example of the disparate way of thinking between CS and MLS folks. CS person says their doing sequencing of a portion of Chromosome #24? MLS says that there is no chromosome #24, there are 22 pairs of chromosomes and a pair of sex chromosomes, unless you're talking about a person with Downs Syndrome or Klinefelter's Syndrome. So if CS sends you a file referencing chromosome #25 to MS, the MS has a few questions to ask. You see CS folks are typically VERY bright, but they don't have the type of training folks in the clinical and life sciences have. And that's the HUGE gap in why EHRs don't work that well, but that's a conversation for another day.

The fact that I spend as much time looking at the results of my programs as I do troubleshooting it, is just the way it is for a newbie like me. And what I hope to do as I'm developing skills in this area, is to create resources that will not only be of use to me, but to others who think like me too.

Now I must get back to doing sequence alignments for a portion of the human chromosome Y, NOT chromosome #25 and NOT a male with Klinefelter's Syndrome either.

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