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.

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.

Computational Astrobiology? Yes!

Biology, Microbiology, Molecular Biology, Bioinformatics, Computational Biology, Astrobiology, and now Computational Astrobiology? Not to mention things like Astrochemistry and Astrophysics and all the other great science stuff out there. Where have I been all these years? Oh yeah, being a computer scientist (or software engineer, if you like). LOL

http://astrobiology.nasa.gov/careers/computational-astrobiology-summer-school-2010-cass-2010/

Protein synthesis: an epic on the cellular level

Bioinformatics Odyssey 2010.11.04

Tonite I have a test over Cellular Reproduction and Inheritance. Next chapter finally is the DNA chapter which we started Tuesday and will probably finish tonite. Yay! Nothing long to post here, no time to think or type, except to post this cool link I just found thanks to a co-worker:

http://ds9a.nl/amazing-dna/

I will be reading this this weekend sometime to see what it's about.

-- Sid

Bioinformatics Odyssey Stardate 2010.10.18

Hello all...

Wow, 30 days to the day since my last post. That says alot about how the course has advanced along rapidly in terms of more complicated material, thus I've spent way more time studying and had less time to even think about writing blog posts. Remember, it's been 23 years or more since I last studied Biology. Phew. I've asked myself a few times, "Sid, what the hell are you doing, man?" in the past few weeks. We've had two tests already and the third is tomorrow. I should be studying.

Thing is, I really do like this class and what I'm learning. It just goes by too fast. I work all day, then go to class, and my brain just wants to relax and I'm trying to make it consume way more new stuff than I ever had in one day of my day job in a long time. But, when I take a few minutes away from the computer screen, and the textbook, I start thinking in pictures about what I'm learning, and it takes me back to why I chose this path... learning about how it is that we're all here.

Since that last blog post we've done chapters on biological molecules, cell structure, and energy flow in cells, and tomorrow's test is on photosynthesis and cellular respiration. I looked ahead and after this we're going to be delving into DNA and genetics, which is the stuff that got me to sign up in the first place. Finally! Tomorrow's test I'm thinking may be the hardest out of the 5 we'll have total in the class, but I could very well end up eating those words on the next test. Surely I'm underestimating the power of the complexity of DNA and genetics, eh? Kinda makes me wonder, after this first quarter, what will be left that we've saved for the 2nd and third quarter of this course sequence? Even more interesting stuff, I presume.

I still haven't had time to play around with any Bioinformatics tools to start getting my feet wet with what's out there, but I'll have some time during the break in between quarters at least. I don't have anything new and exciting for anyone to read in this post. I assume at some point I'll be able to make the blog a more interesting read along the lines of what I had mentioned before, being a resource for other programmers interested in getting into Bioinformatics.

In the meantime, if you're bored, check out the banner ad to the left for the new documentary coming out real soon (and in fact you can pre-purchase on that Kickstarter link) called "DMT: The Spirit Molecule". Or the website here:

http://thespiritmolecule.com/

I wonder if we'll be learning anything about *that* in this course sequence I'm taking.... ;-)

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!

Bioinformatics Odyssey Stardate 2010.09.10

Hello all!

So, it's been quite a while since I posted here. Toward the last set of posts, I was starting to learn about Open Wonderland to try and apply my Java skills to my love for virtual worlds.

Well... things change, and my focus has changed. At that point I was really burnt out on the whole virtual world thing. I've been using Second Life as well as experimenting with other virtual world platforms including Open Wonderland for over four years. I think that area still is in its infancy and has lot of growing and changing to do, and while I'd love to be a part of it, I decided to change my focus. I don't have time to do everything I'd like, and with the technology world changing faster than ever, I decided to change focus to my growing interest in Biology and more specifically, Bioinformatics.

In high school, I took all the college preparatory classes I could, including Biology. At that time it didn't really interest me as a career option. At that point I thought I was either going to be a musician or a psychologist. I've retained my love of playing music, but my interest in psychology petered out soon after high school, and when faced with actually choosing a career path due to the birth of my first child, I chose something I was already good at -- computer programming. Thus began my almost 20-year career in software development.

My current interest in Biology and Bioinformatics actually started outside the computer world, with a book by Jeremy Narby entitled The Cosmic Serpent. The book is a fascinating read about Mr. Narby's travels and experiences in Brazil as an anthropologist, leading him to shamans and visions with ayahuasca. The conclusion is that DNA is somehow "alive" per se, and able to communicate via pictures to those who can see it through the vision. Or so I understood anyway -- it's been awhile since I read it, but I've read it twice and am planning a third trip through it here soon. For more information:

http://deoxy.org/narbystew.htm

http://en.wikipedia.org/wiki/The_Cosmic_Serpent

The Cosmic Serpent on Amazon

So... I started thinking about DNA, and since DNA is information, over time I began thinking about that in terms of my career in information technology. That led me to discover the field of Bioinformatics and all the complementary fields related to it. At this point I assume I will end up in a Bioinformatics position when I complete my studies, but it's possible it might be molecular biology or something else that is more science than code. That would be very cool. When I was a kid I wanted to be a scientist when I grew up. What kind, I was not sure of, other than I was fascinated with Geology at certain points, and I've always loved animals.

I'm 40 years old going on 41 next month, and I can only afford to go to college part-time, but since I had taken classes previously, and can use my IT experience to get out of at least one class, I've got some of my studies out of the way already. From now until May I will be taking Biology I-II-III at Metropolitan Community College in Omaha, and then will start on my Chemistry classes after that, trying to work in what Math I have left along the way as well as a couple other electives required for the Associates Degree. Then it's off to UNO to continue studies for my Bachelors Degree in their Bioinformatics program.

http://bioinformatics.ist.unomaha.edu/

One thing I've noticed is that, while there is alot of information seemingly available for current scientists to acquire the computer skills to do Bioinformatics, there isn't a whole lot of information going the other direction, outside of the degree. I suppose that makes sense since Biology is it's own field and programming is a way to manipulate the information gleaned from Biology. So, since I figure there are others like me that want to specialize their software development skills, I will be posting blog entries as I go along and gain the knowledge needed to work in the field.

This is my first week in Biology I at Metro. We've gone through two chapters of the text. The first dealt with basic concepts of characteristics of life and categorizing life, and the second dealt with some basic chemistry needed to understand the rest of the course. As I mentioned, thankfully I took Chemistry in high school so it's a review for me. Next week we start labs. I suppose people really do set themselves ablaze from time to time in the lab, but I still had to chuckle when the instructor described what to do in the event that happens to any of us.

So, this is it for my first post. I will continue to post on other topics when I feel motivated to do so. I still practice drums religiously and am still going to make music and am still interested in sound and the science thereof, so there will be posts about those things here and there as well to stay true to the title of my blog.

Thanks for reading!

ThinkBalm Meeting : Metrics

Today I attended a ThinkBalm Innovation Community Salon #1 "Is it worth it? A discussion about metrics".

We heard a couple perspectives from participants on what they have done so far in creating and applying metrics to virtual world use in order to justify cost and benefit to determine value in the technology. How much money does it save, does it create new business, does it enhance innovation?

-- one person -- travel costs saved, environmental costs saved
-- is it better than webcams? why not webcams?
-- business community have responsibility to define scientific/business metrics

Group Notes URL:
http://openetherpad.org/WZFQeUn38A

invite:
http://www.linkedin.com/groupAnswers?viewQuestionAndAnswers=&discussionID=18106604&gid=2005729&commentID=15559007&trk=view_disc

Open Wonderland Developer Meeting 2010.04.07

Today I attended the Open Wonderland Developer Meeting. The topic was a walkthrough of the MTGame code.

http://blogs.openwonderland.org/2010/04/07/wonderland-wednesday-mtgame-walkthrough/

I took a few notes for myself although there were some issues getting in initially and then I had to leave before the meeting completed.

Read the MTGame manual for background.

Originally Wonderland was based on Java3D. Then it moved to jME and, and needed thread-safety in that, that we had in Java3D. MTGame divides graphics processing up into tasks that dont require jME (can be done on update threads with single commit thread) and tasks that do.

Looked at classes WorldManager (is client code), AWTInputManager, RenderManager.

Then I had to leave. :-)

Open Wonderland Developer Meeting 2010.03.31

Today I attended the Wonderland Wednesday for 2010.03.31 Edition. This is an Open Wonderland developer meeting. Today's topic was an overview of the jME:

http://blogs.openwonderland.org/2010/03/30/wonderland-wednesday-jme-briefing/

We discussed with the jME developers, various integration topics and what is on the horizon for that. I need to get more familiar with that so I can follow the discussion better.

Next we attempted a discussion of MTGame but had some issues so we are going to get it together for next meeting.

Open Wonderland Developer Meeting 2010.03.24

Today there was another Open Wonderland developer meeting. The topic was a walkthrough of the Sample Module code. The code is here, under the :

It was the end of a long workday for me so I followed along as best I could, and could only attend for the first hour. Luckily Nicole is putting together a video recap so we can review. The couple notes I have for myself to go back and review are:

SampleCellFactory.getExtensions () is apparently a powerful and useful method.

The annotations in the code are important.