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:
Mindforge Tutorial: Try out Linux using Wubi
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 It’s a little outdated, but (probably) still accurate.
Filed under computers/software, HowTo
Mindforge Tutorial: Disk Images
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 you what the big deal is so that your decision to stop reading will be an informed one!
A disk image is a virtual copy of a real disk (so a virtual CD).
That’s it. This is cool because you can make backup copies of your CDs/DVDs (though some have protections that may make this difficult), video games, operating systems, etc etc.
On top of that, you can use virtual CD-drives to play your virtual disks! This has a few advantages: [1] your computer communicates faster with your virtual disks than your real ones, and [2] you won’t have to worry about carrying CDs around ever. Of course, CDs are going the way of the Dodo, so this post may already be useless.
In any event, my middle brother and I once started a custom-PC company called Mindforge Technologies. I made a screencast tutorial for the company that shows how to use disk images, which is the Youtube video above. Enjoy!
Filed under computers/software, HowTo
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 pen!) notes, the idea being that these are more difficult to fake and easier to organize than, say, loose-leaf paper with pencil scribblings.
However, current biological research is done more and more by computer, and a lot of this stuff does not translate well to a hard-bound notebook. For instance, I’m regularly taking thousands of microscopy images (in a single day) for my projects, and printing all of these off would be tremendously stupid. The value of spreadsheets, scripts, plots, and all kinds of computer-generated data is in the fact they they are digital, so why try to convert them to an outdated medium?
Filed under computers/software, HowTo, science
Make Notepad++ your default editor (Windows7)
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 for one: a comment on a more-complicated method. I made the following short screencast to demonstrate that method. This one has the advantages of being easy to reverse, easy to do, and not in any way intimidating!
Filed under computers/software
Python: Monty Hall modeling
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 contain nothing. The contestant chooses one door, but that door remains closed. The host then opens up a 2nd door, and this door is always a losing door. At this point, the contestant may choose to now open the originally-chosen door, or switch to and open the last remaining door.
So why is this interesting? It turns out that the way to maximize your chances of winning is to always switch, and this maximized chance is 67%. It also turns out that this is totally non-intuitive, and that most people think that, if the contestant always switches, the chances of winning are at best 50%. If you haven’t heard the solution to this problem before, you should think through it and see what you expect the chances of winning are under the two conditions: After the contestant chooses a door, and is subsequently shown that one of the other two is a losing door, [1] the contestant always switches to the remaining door, or [2] the contestant never switches. After the jump, I’ll explain this intuitively and then show a Python script to simulate this problem.
Filed under computers/software, 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: http://www.ncbi.nlm.nih.gov/gene
- Proteins: http://www.ncbi.nlm.nih.gov/protein
- Flies: http://flybase.org/
- Yeast: http://www.yeastgenome.org/
Genomes:
- Prokaryotes: ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
- E.coli (for use in this site’s tutorials): ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Escherichia_coli_O157H7_uid226/
Online Tools:
- Protein domain prediction: http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
- Best multiple sequence alignments: http://prodata.swmed.edu/promals3d/promals3d.php
- Not-as-good alignments: http://www.ebi.ac.uk/Tools/msa/clustalw2/
- Translate DNA: http://expasy.org/tools/dna.html
- Primer melting temp: http://www.promega.com/biomath/calc11.htm
Filed under computers/software, HowTo, science
