Tag Archives: biology
cloning trick: ligation of multiple inserts
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
secrecy and biological research
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
LabTeX
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
Filed under computers/software, HowTo, science
useful bioinformatics resources
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
Filed under computers/software, HowTo, science
average gene length in prokaryotes (part 1)
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
Filed under computers/software, science
Notepad++ and Regular Expressions
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 … Continue reading
Filed under computers/software, HowTo, science
Comp Bio frustrations
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 … Continue reading
Filed under science
Interviews
I went to UChicago last weekend for my first round of grad school interviews. It went great, and the grad school environment seems like a great fit for me. However, I’m going to spare details on the schools until I’ve … Continue reading
dinosaurs aren’t animals!
Yeah. I heard that on the radio when driving into Grinnell on Friday. As I was flipping through stations, I overheard a radio “personality” declaring that, in fact, dinosaurs are not animals. Two of her fellow radio people agreed, though … Continue reading
Filed under life
evolution programs
I updated the Weasel program a fair bit, and it is now available on sourceforge. The program still does the same stuff, but the interface is cleaner and friendlier. Most of the changes were just to make the code easier … Continue reading
Filed under computers/software, science
