barralopolis

Pink DNA sequencer at the Genomics Institute in St. Louis.

Once upon a time, in my grad school years, I used to do a lot of microscopy of the fancier kind. At some point, that involved taking care of a deconvolution microscope and the associated Silicon Graphics computer running on Unix. I wanted to be prepared to handle that beast, so I talked to a fellow nerd, who recommended learning Linux. For a few months, I battled with Linux- I installed Red Hat, typed into terminal windows, and learned several commands. It helped a bit when the big machine arrived, but it was not really necessary, so I stopped trying. However, I did notice that it was a skill that impressed certain people.

That pride came rushing back today when we were introduced to Consed, one of the programs dedicated to sequence finishing. It needs to be started from a terminal window typing commands, so we received a short intro about Unix, and I felt pleased that I knew how to do it. It is one of those examples of pieces of knowledge acquired along the way of life.

Today we started officially the second part of the workshop. In the morning we had some free time to practice annotation, which was good. While there is still a long way to go, I could feel that I was getting more comfortable with the thinking behind the analysis, and my speed was hampered only by not remembering which link I had to click on to get the DNA sequence, or the predicted sequence, or whatever piece of information needed. The consensus of the group was that students will need some intense and extensive time to learn the system.

Consed screenshot.

Consed was introduced after we were given a tour of the Genomics Institution, an amazing building with amazing machinery and even more amazing science. We saw the famous pink sequencer, dedicated to the breast cancer genome project. We learned of all the projects the center is involved with, and the gigabytes of information generated weekly through next generation sequencing. Then we were introduced to Consed, and a group of young wizards gave a tutorial about how do they improve the raw sequences.

It was a whirlwind of windows to open, alignments, tracings, tags, comparisons, and decisions to make. However, the program is so visual, that after a while it became almost pleasing to solve the problems with the DNA sequences. Not sure why, maybe because it is more straightforward, but most of us in the group expressed they felt better today than yesterday.

The day flew by again- I get some exercise through a quick morning run in the Forest Park (a joy), otherwise the day is dedicated to work, work, work, with lots of food to sustain us; but we joke about the amount of glucose that we must spend with brain work in the cold cold air conditioned computer room! And it is time to go to sleep again- tomorrow is the last day!

Sunrise over Forest Park.