I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
Build a data set
Align the sequences
Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we' ... Read more
Have you ever wondered how to view and annotate molecular structures? At least digital versions?
It's surprisingly easy and lots of fun.
Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both Windows and Mac OS X. ... Read more
The University of Virginia does.
They survey students every year to find out what they're up to tech-wise. Apparently 99% of their first year students own computers.
And, a large majority of those computers are laptops (3058/3113 or 98%).
And, what's on those laptops? Let's have a drum roll:
60% have Windows VISTA
26% have Mac OS X
12% have Windows XP
and, 2% or less have something else - like Linux.
This is why I really, really, want good web-based applications.
Just for the record, I don't ... Read more
Bio-Link is accepting applications for this year's National Summer Fellows forum, June 2-6th, in Berkeley, CA.
You can get an application at www.bio-link.org
I'll be there, doing some kind of bioinformatics workshop. I'll probably be talking about either metagenomics or comparing protein structures and drug resistance, but if you have topic requests, feel free to submit them in the comments. Read more
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies.
I've been running into this uncertainty myself lately.
I have always known that DNA sequencing errors occur. This is why people build tools for measuring the error rate and why quality measurements are so useful for determining which data to use and which data to ... Read more
I've been writing quite a bit this week about my search for a cross platform spread sheet program that would support pivot tables and make pie graphs correctly.
This all started because of a bug that my students encountered in Microsoft Excel, on Windows. I'm not personally motivated to look for something new, since Office 2004 on Mac OS 10.5 doesn't seem to have the same bugs that appear on Windows. However, I would like things to work for my students. Since I don't want to have ... Read more
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers.
Some of the people who participated in the challenge found out that it was harder than they expected.
Okay, what did we learn?
1. The community is the ... Read more
Okay OpenOffice fans, show me what you can do.
Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned in assignment results with nonsensical pie graphs.
So, I asked what other instructors do with software that behaves differently on different computing platforms. I never did hear from ... Read more
The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college.
More than one person told me that I should have my students install an entirely different operating system and download OpenOffice to do something that looks a whole lot harder in Open Office than it is in Microsoft Excel ... Read more
Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching.
Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It quickly gets to be too exponential.) Nope, sorry, three versions of Microsoft Office on three different operating systems are bad enough.
This semester, I'm teaching an on-line for the first time ever. The subject isn't new to me. I've taught ... Read more