Categories
genetics programming science

DNA Sequencing Moving Too Fast for Computers and Bioinformaticians

Everything in technology seems to increase in exponential fashion.  There’s the ever-quoted Moore’s Law, where CPU speeds seem to double every 1.5 years.  RAM capacities and HD capacities seem to follow this rate, although the correlation might be coincidental more than anything else.  However, network speeds have barely increased in the past decade, it seems. The boon in high-tech, high-throughput technological advancements in modern genetics labs is also a bit of a curse. As the New York Times reports in DNA Sequencing Caught in Deluge of Data:

Categories
general

What are the alternatives to Ubuntu 11.10?

Ubuntu has rolled out with version 11.10 of its distribution (or should we say that Canonical rolled out with Ubuntu 11.10?). This is the second release that features Unity front and center, but unlike 11.04, there is no backup option to allow users to drop back to GNOME 2. To make matters more complicated, GNOME has pushed GNOME 3, also similar to Unity and a complete break from the GNOME 2.x line of desktops. Just as the options for Linux desktop environments is growing confusing quickly, so, too, are the options for a stable, functional distro itself.

Categories
general

Doing Things the Berkeley Way

You’ve got to love the “Berkeley way” of doing things. Not that citizens here think that they’ve really cornered some secret of how to live. They’re just very conscientious and considerate of their place in the world. They live well, but they also let live just as well. Here’s how some things go in Berkeley, and some of the local tips I’m learning as I’m getting myself set up.

Categories
general

Book Review – Version Control by Example

SourceGear is a company that I’ve never heard (until now) that works on version control software.  Eric Sink is the founder of SourceGear, and he has recently written and published the book Version Control by Example.  I came to hear about it perhaps as many others who have seen it already would have — he is giving this book away for free (shipping costs covered), and as his FAQ page says, there are no string attached.

The book covers the history of Version Control Systems (VCS), the terminology and common feature sets, examples of each of those features (in Apache Subversion, Mercurial, Git, and SourceGear’s Veracity), a discussion of how to use a VCS effectively in practice, and details about how VCS’s work internally.  Through following VCS’s throughout history, we are introduced to additional VCS features in a context that easily explains their motivations.

Categories
linux

Could Microsoft make a new Linux X11?

When evaluating Microsoft’s long-term strategic positioning of its core business over the past decade, it is clear to see the cracks that have been forming in a dominating mainstay of the computing world. And it is an instructive story, and one still in the making, about how fast things (businesses, trends, ideas, etc.) can be built and how they can erode just as fast.

And of course, part of the story includes Bill Gates’ decision to bow out, and the ascent of Steve Ballmer’s ascent, notwithstanding the antics, rages, utterances, and more antics. But one utterance I want to pick up on is the one that “Linux is a cancer”. Really?

Categories
general linux web

Can Linux server admin. get better?

Turnkey Linux

After all of the work for a manual installation of WP, when revisiting the Ubuntu Comm. page on WP, I noticed Turnkey Linux, saw their website, and read this Linux Journal review about them. Granted, Ubuntu/Debian is as close to an “It just works” TM user-friendly Linux distro as you’ll find. And WordPress seems to dominate the blogging software scene, and they’ve certain done well to make the installation quite (brain)dead-simple.  But it’s still not as simple as it is to install a Mac app.

Categories
general linux web

Re-installing WordPress on Ubuntu 11.04

Publishing the last post was quite an ordeal, and not because of anything related to the content. Installing WordPress on Ubuntu was a bit more challenging for me than I thought it would be. For those of you who may be running into the same issues I did, here is a run-down of what I did and what I had to change.

Categories
general web

Troubleshooting Unicode in the Khan Academy exercise framework

I started playing around with Khan Academy’s exercise framework. If I am successful in figuring this out sufficiently, the efforts would be applied for teaching a foreign language (Thamil) rather than teaching math. I had gotten the basic case figured out — a single-question, question-answer exercise. From there, I inserted Thamil characters and saved the HTML doc into UTF-16 encoding, and by then, I experienced serious errors. Fortunately, it didn’t take much more than learning the basics of Unicode and a little poking around to figure it out, fix the issue, and get a better understanding of how it all fits together.

Categories
general

Health insurance for the self-employed

One thing that I’ve been looking into recently is health insurance.  Being over the age of 26, I can’t piggyback on my parents’ health insurance plan.  Having most recently worked outside of the U.S., I can’t use the COBRA plan to extend previous health insurance plans.

When you are self-employed, you have a few options.  You can

  1. Remain uninsured
  2. Find insurance through employment
  3. Find insurance through your state or the federal program if you have a pre-existing condition
  4. Buy your own insurance
Categories
general

First post

Hi, everyone.  This is the inaugural post of my blog.

This will be my first foray into blogging — I’m excited!  Do give ample feedback if you can!  Does something work / not work for you?  Do you have followup questions?  etc.

Let me explain the title, “Sequenced Thoughts from Computer / Science”: