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 →
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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 It’s a little outdated, but (probably) still accurate.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 [...]
EVERYTHING but the washer/dryer and bed have been spoken for. Thanks for the quick responses! We have to be out of this apartment by Friday, and need to get rid of this stuff NOW. So, we’re giving it away or making cheap under this condition: The purchaser is totally responsible for getting the pieces. You [...]
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 haven’t posted here for a long time. My brothers and I attempted to throw together another joint blog, but it has proved too difficult to maintain at the moment. I moved over my few posts from there to here today, and must now provide a life update. Since I left off, I went to interviews at Duke [...]
In Seth’s post on dice rolling, he briefly mentioned something called a “while loop”. It has the basic structure while (this is true): (do this) Note: Courier font shows code. A while loop is simple. However, there is an important nuance that you have to understand in order to implement it correctly: any variable defined [...]
Printers are dumb and waste paper. There is little that I hate more (aside from Apple) than having to print a document, sign it, and then scan, fax, or mail the stupid hardcopy. So, I decided to try to cheat the system. Inkscape is a vector editing program that can be used to edit PDFs. [...]
If you’re like me, you love data. Ok, so it’s likely that you aren’t like me, at least in the data-loving regard, but you have to admit that (1) data can be beautiful, and (2) data is how we understand the world. And I really mean you have to admit that; to do otherwise would [...]
Awww… isn’t she the cutest little thing? Python is both a cuddly pet (when in ball form) and an awesome programming language. I’m well aware that most people don’t equate “awesome” and “computer programming”, but that’s simply because most people are ignorant fools. So, unless you already define those two terms in the same units [...]
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 finished all interviews and have started to hear back about whether or not I’ve been [...]
In a previous post, I discussed my attempt to write a program to solve a puzzle. I never updated that post because, well, I ran the program all night and it didn’t find the solution!
I had made up a fake puzzle that I knew had a solution for testing, and the program could solve it [...]
Homeopathy says essentially this: Something that causes disease can be made to cure that same ailment if the something is diluted into water so much that it is no longer present. For example, if you were to take one molecule of cyanide and dilute it into a swimming pool, then drink some pool water, you [...]
Yeah. I heard that on the radio when driving into Grinnell on Friday. As I was flipping through stations, I overheard a female radio “personality” declaring that, in fact, dinosaurs are not animals. Two of her fellow radio people agreed, one kept insisting that they were wrong, and then they asked some guy they were [...]
My mother gave the fam a new game for Xmas called “The Impossible Puzzle.” Or maybe that was the company name. Either way, the label is certainly apt.
The puzzle is composed of nine, 4-sided pieces with interlocking parts in the shapes of the 4 card suits (hearts, diamonds, etc). There is only one way to [...]
I just got an email from the bio department asking me to come for a visit in January (all expenses paid!). That turnaround time was quite unexpected (apps were due just last Tuesday). I’m excited, and I am definitely looking forward to seeing the old alma mater again. I’ll have make time to meet with [...]
Seriously. If I could only eat one thing for the rest of my life, it would be cookie dough. Specifically the Nestle Tollhouse recipe. I was craving it tonight and so I made some, even though I don’t have chocolate chips. I just want the fat and sugar. After I had mixed the butter, sugar, [...]
After a hiatus filled with grad apps, lab work, and Hulu (that awful time-sink), I have decided to get back to writing. Previously, the Brothers and I had been using a joint blog (coster3.com), but I found that this seemed to decrease my posting habits. I’m also pretty sure that the stuff that I like [...]
Life without Internet is like life without water. Yeah, you can live for a couple days but it SUCKS. And then you die.
So, of course, when I moved in to my apartment in St Louis this past weekend, the first thing I thought about was getting access to the series of Tubes. Sadly, all of [...]
I got officially moved into my apartment yesterday. I harnessed the kitten to the passenger door so he could roam a bit, then headed south from Grinnell. I picked up Sam and forced him to help me unload things, then dropped him back off at some raucous WashU event.
All of my stuff was in a [...]
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 to navigate.
BUT, I am currently working on a more interesting program that will model a [...]
So my life has taken and interesting (and welcome) turn lately. I’m applying to grad schools for PhD programs in bioinformatics/genomics/etc, and have found a few schools that have programs that seem perfect. One of those schools is WashU in St. Louis (where Sam is an undergrad).
My mother, grandparents, and I went to visit Sam [...]
This post discusses a computer program that you can download to try yourself (and get the source code if you want to make your own version).
At our huge family reunion (Mom’s side) earlier this summer, we were handed a wordfind that someone had generated somewhere on the Internets that contained the names of the family [...]
(re-posted from coster3.com, the joint blog I share with my brothers)
Inspired by Dawkins’ METHINKS IT IS LIKE A WEASEL program (hereafter just weasel) described in his book “The Blind Watchmaker,” and wanting to practice my blossoming C++ skills, I decided to write my own version of weasel. It was successful enough, and I found the results interesting enough to warrant [...]
I’ve finished the beta version of my METHINKS IT IS LIKE A WEASEL program. I want to tweak it to make it a little more visually pleasing and to add some options for more data retrieval. Or even an ascii graph!
Anyway, I’m posting the code and an executable. If you make any interesting changes (I’m [...]
it is like a weasel.
Apparently this is a line from Shakespeare. I don’t like Shakespeare (I appreciate it, but I don’t like it). This line came up because Dawkins used it, years ago in one of his books, to demonstrate the superiority of selection vs. randomness. He had written a simple program that would start [...]
Now that we’ve got this Mindforge thing (slowly) going, I’ve been trying to decide what path to follow for the next large chunk of my life. I’m still quite confident that I don’t want to do research, though I’d be happy to study biology forever. Alas, since I can’t just be a student for the [...]
Well, I’ve been home for 3 months now and I haven’t finished telling my leaving story! I probably don’t even remember it all now, and I’m sure I’ll end up leaving out all kinds of stuff. I sincerely hope that none of these end up being false memories (my logic may be infallible, but my [...]
So, after getting Mindforge Technologies up and running (ish) my brothers and I decided to go back to having our individual sites. So I’ll be importing the posts I made there over to here. You can read Stoz’s posts at sethcoster.com, and Sqm’s probably at samcoster.wordpress.com, though that may be changing in the future.
Posted in [...]
I am BACK IN THE U.S. And, really, it would be difficult for me to be happier. Really difficult.
Why, you ask?
Well, in short, the Peace Corps wasn’t for me. I joined for selfish reasons and left for selfish reasons.
In long:
11 days ago, on Thursday, I hit bottom. I had only been at site for two [...]
I am BACK IN THE U.S. And, really, it would be difficult for me to be happier. Really difficult.
Why, you ask?
Well, in short, the Peace Corps wasn’t for me. I joined for selfish reasons and left for selfish reasons.
In long:
11 days ago, on Thursday, I hit bottom. I had only been at site for two [...]
3 ish weeks ago my appendix tried to kill me. The lithe bastard pretended to be a stomach ache until he disabled use of my right leg, at which point I spied him, hiding behind my colon, and had the doctor fetch him out.
I had a great time at the hospital. Apparently far too good [...]
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