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!

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.

The Genographic Project : The Human Family Tree

On 2010.03.18 myself, my daughter Jocelyn and her boyfriend Mikey, and my daughter Hayley, attended a screening and post-show discussion for the film The Human Family Tree. The film is a product of The Genographic Project, a long-term joint effort by many scientists and people at IBM. The project as stated on the website, "is seeking to chart new knowledge about the migratory history of the human species by using sophisticated laboratory and computer analysis of DNA contributed by hundreds of thousands of people from around the world." The film is a document about these efforts. Read more here:

http://channel.nationalgeographic.com/channel/human-family-tree-3706-interactive

In the film, the researchers describe how they have taken DNA samples from people on one day on a Queens street, and correlated that with DNA from previous research to chart paths not only of how people of related, but how people have migrated around the world. For example, one black man from America finds he has roots that stretch back through Europe. Things like that don't necessarily make sense to people until one puts the evidence together with lots of other people and finds that we all have common roots starting somewhere in Africa. It's beyond the scope of my post to describe in more detail, but I'd encourage folks to read the background and watch the show.

For $99 you can get your own kit to participate by sending in a cheek swab sample and get your DNA charted in the same way as the people in the film. As soon as I think I can afford it I want to get myself and my kids to participate.

So, do I believe that every human on earth today can be traced back to a small group in Africa? It's believable. The film was designed as an hour and a half to tell a story, rather than an in-depth scientific analysis. There are finer details to how the research was done that were left out of the film that I think could have been included at the expense of some of the storytelling. As with any scientific proposal, I want to dig more into it to a finer level of detail before saying "count me in as a believer".

Assuming the science is solid, what does that mean for me? It doesn't change anything. I think I would feel a deeper connection to other people on the planet, but I've always sort of felt that way after having practiced Buddhism and really exploring what it means to be "not separate". I'm fascinated by the science used. I've been getting into genetics and biology lately and this is a way to take that science and knowledge and apply it. There's something that boggles the mind here that is a game-changer for some people in the way they see themselves fitting into the world, and for others a validation of what they have suspected anyway.

Project Wonderland : Sample Shape Tutorial

Hi folks... Today I am working with a Project Wonderland tutorial on developing a basic module. http://wiki.java.net/bin/view/Javadesktop/ProjectWonderlandWorkingWithModules05 To get to this point I had to download the source and module system code, compile, and test and try them out. I was having problems for awhile with errors in the server output. Eventually today I figured out that in some cases when the server doesn't shut down properly, read and/or write perms on some log files may be hosed and prevent proper startup next run. Here's me trying out the PDF Viewer module, before I go off on the current tutorial material.

And here's me after completing the steps in the tutorial to download, build, install, and test the shape sample module.


Pretty simple! So my next steps are to:

1. Generate ideas for what I would like to create a module for.
2. Continue inspecting the server logs and code in order to keep getting more familiar with the inner workings of the infrastructure.
3. See what work has been done or is being planned on things like application performance and monitoring.

See ya next time!

Death and My Blog

Hi folks...

Perusing my blog here, while there are few posts relative to the timeframe I've had this thing, I'm proud of myself for having a blog in the first place.

I'm a seeker... a seeker of knowledge, of new and different and more productive ways of doing things, of new music, and alot of other things. I was initially skeptical of blogging in the first place, as I didn't just want to go start a blog just to have one. After some time I finally found a good reason. I began this blog to document my research and experimentation with some new technologies that have rekindled my interest in what is possible with computers and technology, a field I've been in for a long time.

I look back on the relatively few number of posts and think, "well, maybe I don't have the motivation for a blog that I thought I had"... However, I am thinking tonite and realizing it's not about the blog. It's about my motivation to work on the projects that interest me. Without getting too personal, let me just say that I've had lots of motivation in the past in my day job. While I don't have a dream job, I've had a pretty nice ride in the industry, having been unemployed only a week and a half out of almost 19 years. I've seen alot of cool things, some came and went, others stuck around for the duration. I think, as alot of others do, that we've only begun, relatively, to delve beneath the tip of the iceberg to what technology is going to do in transforming humanity. Had I known it would get to this point so soon in my career, perhaps I would have been motivated even more before to dig deeper myself. Honestly though, alot of computer stuff comes easy to me. That's not to brag, it's just that I've a talent for it is all. But unless one really strives to push the limits of whatever talent they have, it seems to turn to boredom at some point. I'm guilty of that, and the reasons are my own, and I won't make any excuses. That's not the point of this writing.

The point of this writing is for me to take an honest self-assessment of where I'm at, in order to try to push the envelope on my talent into new territory. You see, in 2007 and 2008 I turned on to virtual worlds. I was all excited, even buying a sim in Second Life so that I could meet people, have a place to build, script, and develop a new set of skills in an area of technology that was, and still is, new and exciting. Throughout 2008 I became a pretty good scripter in Second Life and OpenSim. I worked on the side for a project at work that provided great experience and contacts but ended up not getting off the ground as the technology hadn't matured enough yet for what we were trying to do. And since I was a Java programmer by trade, I became very interested in Project Wonderland and the possibilities there, since I could readily apply my skills.

At the end of 2008, my younger brother, who was a little over a year younger than me and whom I spent a lot of time with, passed away. Shortly thereafter, I sold my Second Life sim as I couldn't afford it anymore. I also lost a lot of the motivation I had. I felt lost and empty, to say the least. Insert all relevant things about death of a family member whom one is close to here, et.al. as I've run the gamut and continue to deal with it. I think the strange thing is that I am just starting to realize how much my brother's death has had an effect on me and not only my work, but my motivation in general. In fact, one of the most surreal things to me is how calm things seem nowadays, as though I could do anything I wanted in life if only I apply myself, and yet, what is it that really matters in the end? In say 5, or 10 years, what do I want to look back on and say, yeah, I'm glad I did that? Insert all relevant sayings about how the journey is the reward, et.al. here. ;-) I suppose some of the surreality is due to the nature of the time my brother and I spent together and our relationship in general. Those are personal things that again I'm not going to get into here. Thing is, I thought at some point last year I picked back up to normal speed with my life. The reality is that the love I had developed for the technologies I am interested in had waned, and I was looking everywhere else for reasons why, except looking at where my motivation had went.

I may wake up tomorrow thinking the half hour I spent writing this blog post was a waste of time. I probably won't though. I know that even though I can't explain why my brother no longer exists in corporeal form, I can continue to seek knowledge and truth about the experience. In the same way, I think I must get back on the path to greater knowledge in the technologies and research areas that I love. Technology is always changing and while I can't predict the outcomes, I can spend some time each day seeking knowledge and learning. As I like to tell my friends when I want to go to the store, I just want to see what they got. ;-)