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!

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.

Open Wonderland Developer Meeting 2010.03.21

I attended the new Open Wonderland Developer Meeting today. Today the topic was an overview of the source code hierarchy in NetBeans, and when my client was off in the weeds I recall discussion of the core and web hierarchies as well as some debugging hints.

Next meeting is Wednesday 3/24 but I forget what time so I'll have to check the Wonderblog.

http://blogs.openwonderland.org/

The topic for next meeting is an overview of the module tutorials I believe. That will be a good review and a chance for me to get more familiar with the code. I completed the first two tutorials but didn't get a chance to poke around much. Also, developing with an IDE is new for me. I've always been a command-line type of guy and probably will stay that way, but I don't see that it will hurt having skills in both methods.

Open Wonderland User Meeting 2010.03.20

Today there was an Open Wonderland Community meeting. It was announced on the Facebook group. If you're interested in Open Wonderland, join the Facebook group!

There is a Cafe Press store now that people can buy things from with some of the proceeds going to the foundation. As of today there is 1 item but there will be many more to come.

http://www.cafepress.com/OpenWonderland

There is an Immersive Education Summit coming up in April that the project team is looking at attending.

There was some discussion around an 0.5 Preview 4 release. What is needed as a foundation is a process for deciding when it is time to put out a release. There is also a forum thread on this topic which goes into more detail.

http://groups.google.com/group/openwonderland/browse_thread/thread/ff2986e3308e3d62

There will be a new "help wanted" link from the project page pointing out where the team could use help with things. I'm looking forward to that.

There is a regular developer meeting in the works which will be announced once it is organized. This will be a separate, more technical, meeting to complement the more general community meeting. It sounds like the first one will be tomorrow so I hope to attend.