Bioinformatics Odyssey 2011.03.21 INFO1100 Week 2

This week is on Module 2, "Gene Structure and Information Content", and Module 3, "Nature of Chemical Bonds".

Module 2

mRNA cap and tail - methyl guanosine cap and 150-200 adenosine ribonucleotide tail

mRNA 250-10k nucleotides, ephemeral

tRNA/rRNA mechanism

Resource reviews:


http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a1.html

http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html

http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a3.html

tRNA is RNA coiled up into the proper shape for the transfer activity



http://www.johnkyrk.com/DNAtranscription.html

mRNA cap and tail - methyl guanosine cap and 150-200 adenosine ribonucleotide tail

mRNA 250-10k nucleotides, ephemeral

tRNA/rRNA mechanism



http://learn.genetics.utah.edu/units/basics/transcribe/

basic transcription activity


http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf

basic flash show


http://nobelprize.org/educational_games/medicine/gene-code/flash/code.html

game cant get to load


http://www.bioscience.org/atlases/genecode/genecode.htm

form for finding amino acids


http://www.learner.org/courses/biology/archive/animations/hires/a_genom6_h.html

need sound, do later

http://www.youtube.com/watch?v=983lhh20rGY

need sound, do later

Introduction to Bioinformatics Week One

I am sitting here in my first day of my Introduction to Bioinformatics course at Metro's Sarpy campus. The class meets Monday afternoons from 1 to 5 pm. The instructor informed us that the format of the class is independent study and that we will meet and lecture for about an hour, and then the rest of the work is up to us. Homework and quizzes for each week are all due by 11:55 PM on the Sunday before the next class. Sweet! I could leave if I wanted to as 2 of the other 3 people in the class did, but it's easier to just sit here and complete the class work here.

I thought I'd use the blog to document my work and thoughts as I'm doing the work. We'll see how it goes.

The lecture today was a review of the Human Genome Project and DNA and RNA chemical structures and operations.

First up, a review of the Human Genome Project educational CD:

http://www.genome.gov/Pages/EducationKit/download.html

There is a ton of information here, not enough time to read it all. But while looking at the 1953 year in the timeline about Watson-Crick, I decided to go find their journal article online.

I happened across the following link:

http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397

It summarizes a broader length on the DNA timeline, and how all the pieces fit together.

Next up, a review of the Genome On-Line Database.

http://www.genomesonline.org/

A presentation about Gene Prediction, which soared way over my head about 10 pages into it ;-)

http://cbis.anu.edu.au/bioinfosummer-2003/tuesday/13h30-14h30_speed_keynote.ppt#4

A Science magazine article, "Realizing the Potential of the Genome Revolution: The Genomes to Life". This talks about...

The link is available to journal subscribers only, but here is the link anyway. I was able to access it via Metro's online library mechanism.

http://www.sciencemag.org/content/300/5617/290.full.pdf

A phat flash presentation on contents of a cell:

http://learn.genetics.utah.edu/content/begin/cells/insideacell/

1. Realizing the Potential of the Genome Revolution: The Genomes to Life: http://www.sciencemag.org/content/300/5617/290.full.pdf
2. Inside a Cell: http://learn.genetics.utah.edu/content/begin/cells/insideacell/
3. Reverse and/or complement DNA sequences: http://arep.med.harvard.edu/labgc/adnan/projects/Utilities/revcomp.html
4. Tour of the Basics: http://learn.genetics.utah.edu/content/begin/tour/
5. Nova Online: http://www.pbs.org/wgbh/nova/genome/program.html

Omaha Dynamic Language Users Group 2011.03.08

On 2011.03.08 I attended the Omaha Dynamic Language Users Group meeting.

http://odlug.org/

This was my first meeting with the group. I've been wanting to attend for about a year but have had class on Tuesdays for the last 6 months. With a break in the action from quarters at Metro I was able to hit this meeting as well as the OLUG meeting last week. The only bummer is I'll miss out on the trifecta this month since my class fires back up again tonite and thus I will be in class next Tuesday when the OJUG meeting is held.

Anyway, tonite was a great meeting. I met a couple new folks and was introduced to some new things I hadn't seen before.

Jay Hannah presented Test Driven Development in Perl. If you're not on the mailing list:

http://groups.google.com/group/odynug

then the code for his presentation is here:

svn checkout https://clabsvn.ist.unomaha.edu/anonsvn/user/jhannah/UNO/Perl_TDD_Intro


I've done unit testing before, and sometimes it was test-driven, other times it was catchup-driven. That was all in Java, though, so it was nice to see Perl mechanisms for accomplishing this. Also I hadn't heard of TAP, or "Test Anything Protocol":

http://testanything.org/wiki/index.php/Main_Page

which in a nutshell is a protocol for formatting between test mechanisms. For example, I could take the output of my Perl tests and read them with the TAP C interface, if I wanted to do that for some reason, perhaps if my main harness was in C and I wanted to combine output into one file, for example. I *think*, anyway -- if I got the gist of it right. I didn't delve too deeply into the specifics but that's what I got out of the cursory intro and peruse of the doc.

Next up Scott Hickey presented from chapter 5 of the Land of Lisp book. The example was a text-based sort of role-playing game, so we got to see what Lisp looks like and how some mapping of functions onto data works. Or as Scott puts it -- "MapReduce in the small".

So I am looking forward to June when I am hoping to take only online classes at Metro so my evenings will be freed up again and I can shoot for a monthly user group attendance trifecta for the summer months!

UNO Biology Department Second Annual Graduate Research Symposium

Today I took the afternoon off to go visit UNO for the Biology Department's second annual Graduate Research Symposium.

http://avalon.unomaha.edu/biology/symposium.php

Even though I'm still early in my studies I was able to understand alot of what was talked about. For example, there was some discussion of DNA and RNA and nucleotides, and use of electrophoresis in some of the research and I knew the basics of that from my Biology I class at Metro.

I took a few notes on some things I wanted to look up, that I didn't understand, that I will post here later.

DNA Sequencing with Nanopores

The IBM solution which I may have linked to before, uses holes in silicon chips:

http://www.wired.com/gadgetlab/2009/10/dna-analyzer-on-a-chip/

and here's an approach using an engineered protein called MspA:

http://www.scientificcomputing.com/news-HPC-Jaguar-Supercomputer-Helps-Develop-Affordable-Personal-Genome-Sequencing-022811.aspx?et_cid=1207025&et_rid=41428335

Base Pairs : Watson-Crick and Hoogsteen

http://www.astrobio.net/interview/3761/an-alternate-dna-structure

Omaha Linux Users Group 2011.03.01

Tonite I attended the Omaha Linux Users Group meeting. For the scoop about the group:

http://www.olug.org/

And the entry for tonite's meeting:

http://www.olug.org/2011/02/march-2011-olug-meeting/

See the stream:

http://www.ustream.tv/recorded/13031513

LibreOffice, which I didn't know about, is a fork of OpenOffice. I already use OpenOffice so it looks like it may be time to move ahead a little more into the future by installing this now.

http://www.libreoffice.org/

GMail backup would be nice to implement. In the pre-GMail days, I used to download my email and attachments and keep them around for some reason. I keep thinking I should do that with my GMail someday, but never get around to it. This past weekend a very small percentage (although in sheer numbers, alot, around 150k) of people's GMail accounts archived email disappeared due to some technical glitch. They have backups and are restoring. The tool that was presented tonite was called "getmail":

http://pyropus.ca/software/getmail/

http://www.mattcutts.com/blog/backup-gmail-in-linux-with-getmail/

We also discussed Gnome 3 which at first glance, to use Jon's terms, looks very "app-y" -- very much like my smartphone interface.

http://gnome3.org/

It could be cool. However there are some quirks that while they may seem small at first, seem weird to me. There's no "restart" option in the system menu, for example -- does that mean the system is supposed to be so stable that you'd never need to actually "reboot", per se? I understand simplification but... hmm... also things like, they were supposed to be doing away with the minimize/maximize buttons on windows. Then the idea was that maybe those things are to be customizable by distro, so if you have a full-blown desktop edition, say, then you'll have some of those things you're used to (and kind of need).

There was talk of some other smaller things that weren't on the agenda. One is this Android Notifier:

http://code.google.com/p/android-notifier/

It runs on the desktop and is supposed to show popups when events happen on your Android phone, like for incoming calls, texts, battery level low, etc. However I couldn't get it to install on my G1, and I tried twice while at the meeting. I get the feeling it's because I still have the Android 1.x and it requires 2.x or something, but haven't delved into it to find out yet.

One other thing was the HTTPS Everywhere browser add-on:

http://www.eff.org/https-everywhere

You plug it in and for a list of sites, it automatically turns on HTTPS so you don't have to think about it.

This was my first ever OLUG meeting. It was cool and I will go back when I can, though my Biology class next quarter is going to hold me out for a few months yet since it is on Tuesday and Thursday. Next Tuesday it's off to my first Omaha Dynamic Language Users Group meeting:

http://www.odlug.org/

And then I will remain wishing I could hit OJUG until after I don't have classes on Tuesday evenings again:

http://www.ojug.org/

That's all folks.