SQL
sporte | August 6, 2008This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
But first, we have to answer a different question about which parts of their reads are usable and which parts are not. (A read is the sequence of bases obtained from a chromatogram file.)
How does our data get…
sporte | August 4, 2008What happens when high school students clone and sequence genomic DNA?
Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of…
sporte | February 16, 2008I love the way you show me secret things.
All I do is type: Select * from name_of_a_table
And you share everything with me.
Without you, my vision is obscured, and all I see is the display on the page.
In fact, this was the push that finally made me decide to learn SQL.
In our bacterial metagenomics experiment, I realized that my students could use FinchTV to enter their blast results into our iFinch database.
That was cool, but with the web interface, we could only view one result at a time.
On the other hand, if we use the right SQL query in the iFinch query window, we can see…
sporte | February 11, 2008One of my chief joys in life, often to dismay of others, is working with data. Some members of my family (who shall remain nameless) would characterize this fixation as bordering on obsessive, others just call me a "geek" and leave it at that.
I don't care.
Give me a data set and I can play happily for hours. The sky gets dark. The dog entreats me over and over to please throw her sopping toy so she can go chase it. The cats walk between my hands and the keyboard and rub their bodies against my face.
But I don't see any of that when there's a computer screen in front of me and columns…
sporte | February 9, 2008A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise.
Well, I've changed my mind in one respect. Most biologists need to work with some kind of database these days and I've discovered that it's really helpful to know something about SQL. Even a tiny bit of SQL, like "SELECT * from table" goes a long, long way.
This revelation didn't happen overnight and when I decided a few…