Bioinformatics Odyssey Stardate 2010.09.18

Hello all...

This weekend marks the end of week two in my first quarter back at Metro in pursuit of a Bioinformatics degree. Last week sometime I sat down and mapped out a hypothetical class schedule and order for the classes I have left to get the Associate of Science degree at Metro for transfer to the University of Nebraska-Omaha. It puts me at the end of the 2011 winter quarter, optimistically, assuming I can handle taking a Calculus class at the same time I'm taking a Chemistry class -- I work full time, at a salaried, job, where overtime is fairly mandatory. *sigh*

However -- on a positive note, I think I may be able to dive into messing around with some Bioinformatics software real soon. My previous research on the subject pretty much told me, "well Sid, you're going to just have to bite the bullet and learn Biology again from scratch", since it's been over 20 years since I last knew what it meant for an amino acid to be a building block of protein, and a nucleotide a building block of DNA -- wait a minute, did we know about DNA back then? LOL Oh yeah, Frances Crick and James Watson figured it all out in 1953, I forgot (thanks to Wikipedia's DNA entry!)

Two weeks of Biology I doesn't sound like near enough to do anything with Bioinformatics, to you -or- to me, mind you. But for fun anyway I decided to crack open the Bioinformatics for Dummies book I bought last year, and now I understand what it's talking about. By the way, this is the first, and hopefully last, Dummies book I will ever buy. That's not to say that there's anything wrong with them. It's just that they're not my cup of tea, really, and generally in my day job when I need to know something, I go consult the real manual on it, instead of something like this. But I bought this thinking it might be a good bridge to take me from where I was at at the time, which was having not had an ounce of Biology knowledge inserted into my brain since the late 80s, to where I wanted to go, which is using Bioinformatics software and seeing what I can find out with it and try to make it the focus of my career in a few years. Well, I was sad to find out that it didn't quite cut it -- I was still going to need some basic Biology knowledge in order to do what I wanted to do. In other words, I was not just a dummy when I bought the book -- I was an uber-dummy when it came to Bioinformatics. Hence, me going back to college.

Here's the good news -- while I won't be doing heavy duty Bioinformatics research tomorrow, or even next week, perhaps not next month, the things I need to be able to start playing around with the software and data banks, I feel like I have now and can start mucking around again. In this way, it will be a sort of complement to my class material, to help reinforce my learning and grades.

Let me stop here and explain what I'm jabbering about for a moment. There is an excellent online resource about the Human Genome Project with a great section about Bioinformatics. To quote from that resource:

"Bioinformatics is the branch of biology that is concerned with the acquisition, storage, and analysis of the information found in nucleic acid and protein sequence data. Computers and bioinformatics software are the tools of the trade."

The resource is at:

http://www.genome.gov

and the specific Bioinformatics section:

http://www.genome.gov/25020000

So I've acquired a basic knowledge of nucleic acids and proteins, and with my software development skills, I hope to be able to see what I can see. At this point of course I still have a long way to go in Biology to really begin to even formulate a picture of what I might want to look for specifically, and to be able to understand what other people are really looking for. But, all the better. My brain is becoming spongy again, ready to learn and partake, and I'm hungry to find something really far out to code for. I know BioPerl is big, and there's also BioJava, both of which I've got a good deal of experience with.

I'm going to wrap this post up now. I've got my first test in class on Tuesday and I spent most of today finishing my notes and studying. I imagine I'll spend a good amount of time tomorrow and Monday studying again, but hey, I will be ready come Tuesday. Talk to y'all later on!