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.

Next-Gen Sequencing Software Technology Clinic

I usually don't attend these type of things. For one, I have enough work to do at my real job during the day. Half the time these are just marketing things anyway. When they're not, then I prefer to just read something, which takes far less time than sitting on the phone. I attended today's because it was hosted by Kevin Davies, author of "The $1000 Genome" book, which I am considering purchasing.

Speakers:

1. Chris Dwan, BioTeam

http://blog.bioteam.net/

2. Tom Downey, Partek, Inc., St. Louis

www.partek.com

for copy of slides: inquire@partek.com

3. Matthew Kayser, DNASTAR

Product lines focused on desktop computer

4. Michael Kuzyk, GenoLogics

RapidScripting API

www.genologics.com

5. Clifford Baron, Accelrys

accelrys.com

Complexity of data analysis are greatest hurdle to $1000 genome

Some terms to research:

reads -- short and long
SNPs
assembly
mapread
inversion
indel
CNV
expression factor
exome

Other

The symposium will be archived and available online for 90 days. I will post the link here when I get it.

More Games

FoldIt, EteRNA and Galaxy Zoo

RNA : The Game

http://www.astrobio.net/pressrelease/3742/rna-the-game

I know there are other scientific games. I will review these in an upcoming post.