Field of Science

It's all coming back to me...

My goal of using the Gibbs motif sampler to examine the consensus of USS repeats in other genomes is getting closer.

This morning I found the Perl script we wrote to chop genomes into sub-segments for Gibbs analysis, figured out its requirements, and used it to prepare a Neisseria genome sequence for analysis. I worked out where I needed to put the resulting genome file in my directory on the computer cluster server, and used Fugu to do it. I found the instructions on how to log on to the cluster from the Mac Terminal, found my password, and figured out how to change to the directory with the Gibbs program in it. I worked out how to modify the command line to work for this genome, and YES! it worked.

Unfortunately it didn't readily find the Neisseria USS motif, even though it's a much simpler motif than the H. influenzae one, and a bit more frequent too. I'm hoping that by tomorrow my brain will have remembered how I solved this problem for H. influenzae.


  1. In an ideal world, all of us would document everything that we do, when we do it and store it all safely. None of us live in that world though.

    Still - this is a great use for a wiki. Do you guys have a lab wiki, or any plans to add an open wiki to your open blogs? That would be great to see.

  2. Unfortunately I developed my research documentation habits with paper and pen. So my benchwork is quite well documented (not 'meticulously', but pretty good) but the bioinformatics is not so good. I think the problem isn't just my habits, but also the nature of the work.

    We have a wiki but haven't got into the habit of using it for nanything. Maybe I'll blog about that.

  3. It is difficult to document bioinformatics work, which generally consists of output files. There are solutions around that programmers use (CVS, Subversion, Trac and so on), but your "average" biology lab would have to be pretty keen to go there.

    I think the nice thing about a wiki is that it's relatively easy to set up and then you can simply use it as a dumping ground. Even if you just upload scripts, files or whatever into it with minimal comments or explanation, at least you know that it's in there somewhere.


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