A few days ago I found myself have a vague recollection of a statistics problem presented at some unknown level in my education. All I could remember was that it had to do with having a room full of people … Continue reading →

I’ve spent the last couple months building a plasmid library, and in the process I thought of a trick. Ligations, perhaps the worst part of cloning, are notoriously finicky reactions. The goal is to take several pieces of linear DNA, … Continue reading →

It is becoming increasingly clear to me that my ideal picture of “doing science” is following the fate of all ideals: death at the hands of reality. While I was working away at WashU, preparing for graduate school, I imagined … Continue reading →

As part of the continuing closet-cleaning series: WindowsXP text is ugly and induces eye-pain and headaches. Here’s what you can do about it:

Still cleaning out the closet… I made this video tutorial a couple years ago for my brother‘s and my short-lived computer company. It’s a little outdated, but (probably) still accurate.

If your first thought, when reading the title of this post, was “What in the hell is a disk image?”, you probably aren’t alone. But before you decide that you don’t care enough to read on, let me quickly tell … Continue reading →

Lab notebooks are the linchpin of any scientific endeavor, since they serve as proof for everything that an investigator has done (and as a personal reference for long-forgotten protocols). The standard is to use a bound notebook with handwritten (in … Continue reading →

I previously showed you (without a screencast) how to make NP++ default in XP. Of course, people have successfully done this for W7/Vista as well, but the various tutorials I saw were all a huge pain in the ass. Except … Continue reading →

You’ve all heard this classic statistics problem, based on an old game show: A contestant is shown 3 doors. Only one of those three doors hides something of value to the contestant (perhaps a new car), while the other two … Continue reading →

I’ll try to keep this page updated with the kinds of things that I’m familiar with and find the most useful. The resources in this list will be used extensively in tutorials on this site. General Genes:       … Continue reading →

One of my side research projects involves processing large numbers of genomes (specifically, all fully-sequenced prokaryotic genomes). Since I’m playing with the data anyway, sometimes I end up with random questions that can be answered with what I already have on … Continue reading →

For the low-low fee of $15/year, you can have your very own custom CSS document to make your WordPress blog exactly the way you want it! A CSS file is just a text file, at MOST a few kilobytes. In … Continue reading →

What follows is from an old post I wrote on replacing Windows Notepad with Notepad++, but is just the part where I ramble about how amazing it is and why you should use it. To get to the post on Notepad replacement, go here. If you ever use Notepad, Windows’ native text editor, you should [...]

While perusing a bookstore a couple years ago, I stumbled upon a fascinating book by Douglas Hofstadter called Godel, Escher, Bach. If you like math, biology, music, art, computer science, and philosophy, this is really an amazing read (though I admit I’ve only gotten halfway through in all the time since I bought the thing). [...]

Some simple, hopefully useful, and totally non-optimized functions for working with nucleotide sequence data (note that there are many more tools as part of the biopython distribution, if you’re interested in learning the library) : First, for cleaning up a sequence (preferably in FASTA format): def clean_sequence( sequence ): """Given a sequence string, return a [...]

A few years ago I wrote a post on making Notepad++ your default text editor, wherein I expressed my extreme love for this little piece of open source software. To date, I use it for just about everything and, after extensive use in a computational biology lab rotation, I figured I should share one of [...]

While working on a little Python script to do  some datamining for lab, I stumbled upon a serious problem: When connecting to the Internet via the school’s network, whether hard-wired, wifi, or through VPN, I could not get Python to fetch webpages using urllib.request. Here’s the quick solution to anyone else with that problem (for [...]

I’m working on a post on the awesomeness of Regular Expressions, specifically in Notepad++ and for use on FASTA sequence data. Check back soon (if you care…)! Filed under: life Tagged: fasta, notepad, regular expression

You (the passenger) are trying to get onto an airplane; Terrororists sometimes try to get onto airplanes; Therefore, you might be a terrorist. Filed under: life Tagged: airplane, flying, logic, tsa

I finished up my first lab rotation two Fridays ago, here at UT Southwestern. It was a pleasant few months with an interesting project, consisting mostly of starting at a computer screen and writing Python scripts, running BLAST searches, and so on. To summarize, but leaving things vague (both for most-people-don’t-care reasons and the-data-is-unpublished reasons), [...]

I have now totaled 96,000 views (mostly on the companion cube cake post, followed at a distance by the LaTeX posts) over 194 posts and received 212 comments. Every time I see that number, 212, I immediately think of boiling water (it is, after all, the boiling temperature (in Fahrenheit) of water). When looking at my blog’s stats, after [...]

I’ve been back in Grinnell for a week, and have another week left before moving to Dallas and into my first real home. My now-fiancee (then-wife) will be joining me, and will be going back to medical school as I start my graduate program. We’ll be closing on the condo Thursday, getting married on Saturday, [...]

I have been often frustrated by the difficulty of searching for solutions to my LaTeX and R problems. Google keywords have to be carefully chosen in order to not find sites relating to latex rubber (in the first case) or everything with the letter ‘R’ in it (in the second case). Fortunately, I’m logged into my [...]