Today I got to teach my new bioinformatics lab. It was great! Well, it was pretty good anyway. The TA who was supposed to teach one of the labs this morning didn't show up and the staff were casting about for anyone who could cover the lab, so I volunteered. It was nice to get a chance to teach the new lab first hand and see how the changes worked. The lab has an interesting history...
When I first came to UMass, Eric Martz was presenting a workshop on molecular visualization. The workshops were aimed at faculty who wanted to develop illustrative materials and tutorials on 3D visualization of macromolecules using Rasmol. I sat in on the workshop and was interested to learn about the software and how it worked. Afterwards, in chatting with Eric, I pointed out that my only criticism was that I wasn't sure what students could "do" with the software. It was easy to see what an instructor could use it for: you could tell students a bunch of stuff. It was less evident how students could use the visualization software to explore and discover useful regularities about macromolecules.
Since that time, Eric has gone on to create 
Protein Explorer, an incredibly powerful set of scripts that provide a framework for interacting with Chime, a browser plugin based on the Rasmol codebase. I had continued to scratch my head and try to think up some activity where students could use the 3D view to discover something. (OK, as time has gone on, I've also learned that there is a lot students can discover about molecules simply by exploring them in an open-ended way, but still...)
About three years ago, at the bioquest workshop, I had an inspiration. I had just learned about the Biology Workbench. I learned how to run a blast search on a protein and perform an alignment. Someone pointed out how the conserved regions, that were scattered along the sequenced, might all cluster around a particular site (the active site) on the 3-dimensional structure. The light bulb went on. When I got back I found Eric Martz and described to him what I wanted. I wanted a way for students to be able to traverse a sequence and color in each amino acid with the same colors that were used in a boxshade of the alignment. That fall, we ran the activity for the first time.
It was hard. Students had to perform a search (to find the initial sequence), perform a blast search (which required setting some parameters), thoughtfully select homologous sequences, use CLUSTALW to create an alignment, use BOXSHADE to make a printed diagram, and then go along each amino acid in the sequence and color it in. When I taught it, students were challenged but in the end, gave the lab a round of applause. They said it was a great experience and that they learned a lot. The TAs hated it. When they taught it, students got lost. Some TAs actually told their students that the activity didn't make any sense and that they should just leave.
The following year, in the face of overwhelming criticism, I redesigned the lab. The TAs wanted more comprehensive directions: click here, click there. Then they said that students complained about how the lab was just a lot of clicking. We redesigned again. By this time Eric Martz had created MSA-shade: a Protein Explorer module in which you could just paste an alignment into a field, and it would color in the sequence automagically. Unfortunately, it only "mostly" worked. Sometimes, the alignment didn't match up properly with the PDB file and you'd have to make manual adjustments. That was too complicated.
Around the time the lab was running last year, Consurf appeared. Consurf did everything: blast search, alignment, and coloring in. This year, the lab has been reduced to 6 clicks. Click here to look at an enzyme in 3D. Click here to compare it with a homologous enzyme. Click here to compare it with a an analogous enzyme. Click here to see the conserved regions. Click here to look at another one. Give a little report. Whoopee.
The TAs are grateful. The lab coordinator is grateful. The students seemed to think it was OK. Some of them were drifing off to sleep about two-thirds through the lab. But at least they didn't complain. It was nice to actually teach it myself and confirm that it really is OK. I had created all the results at consurf ahead of time, but hadn't had time to look at the results and I was pleased to see that some of the molecules show really striking conservation around the active site. Everything worked OK. I'm still just a little depressed.