Week+of+9-21-09

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 * 9/21/09** I spent about an hour downloading Jing and going over the tutorials and doing a little practice with it.

=**9/22/09**= I continued doing some work getting used to Jing, and then I decided to use it to help illustrate my research using it. While not essential or even terribly useful at the moment, I feel that getting familiar with it now will obviously help me focus on the new subject matter once I start working on the project in earnest.

So pretty much because I can, here's a picture of the Bioinformatics main page: Obviously, this sort of thing will likely prove quite useful once I start getting things of my own underway. But for now, it's just cool, and more importantly, good practice.

Having been over most of the bioinformatics site already, I turned my attention to the more detailed side of the research. I started with the specific steps listed in the previous student's milestone page, found here. The first step on the milestone map is to build up a more solid background on the biology, chemistry, and terminology involved in the project. The page itself is linked here. The previous student felt that it was particularly important to know about peptide bonds, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), hydrophobic interactions, and plasma membranes. While I knew much of this information beforehand, it never hurts to have a refresher, and I did learn some new key points as well, listed below:
 * Peptide bonds are partially double-bonded, making them rigid and planar.
 * RNA backbone (the part which the bases are connected to) is composed of C-1 of D-ribose, which links to the phosphate via the C-5 hydroxyl, and the polymer chain itself is linked across the C-5 to C-3 gap by phosphate groups.
 * DNA sequences are read in the 5' to 3' direction
 * Clusters of molecules with hydrophobic components, which, when in an aqueous solution, form clumps (to maximize polar regions pairing with the water and the hydrophobic regions with each other) are called micelles, and are stable structures of amphipathic compounds (which Google tells me means that it has both a hydropohbic and a hydrophilic component)

Much of the terminology of these pages assumes a heavily biology and chemistry-literate background of the reader, and I am not sure if this fits with the purpose, format, and philosophy of the wiki in general. I myself was a bit confused at points, which means that students who have not taken classes that I have would almost certainly be confused. While highly informative, the page could be modified to be more accessible to the average reader. If this is desirable, I would like to copy the page and modify it, placing it in my logbook for future reference, and so as to avoid duplication of efforts. While the anonymous basis of the wiki does not allow full citation, I would of course specifically address that a good portion - if not majority - of the credit belongs to the previous student. If TL or another viewer could discuss this option on my logbooks discussion page, I appreciate it.