On to other manuscripts!

My bioinformatics colleague is headed back home, and our uptake sequence manuscript is waiting for the last bits of data, and for me to write a coherent and thoughtful Discussion. It's not nearly as far along as I'd hoped, but it's a much better piece of science than it was shaping up to be a week ago. One key step was switching the axes of a couple of the figures. Seems like a minor thing, but putting "% sequence identity" on the X-axis rather than the Y-axis transformed the data from meaningless to crystal clear.

The only big piece of analysis we still need is an examination of which of the H. influenzae genes that don't have BLAST hits in our three standard gamma-proteobacterial genomes also don't have hits in the more closely related A. pleuropneumoniae genome. Those that don't are stronger candidates for having entered the H. influenzae genome by horizontal gene transfer, and we predict they will also have relatively few uptake sequences.

So what's the problem with the Discussion? I don't seem to be able to see the big picture for the trees, and I'm hoping that setting the whole think aside for a couple of weeks will let the fog dissipate.

Lord knows I have lots of other stuff to work on. I wish I was going to do some benchwork, but I'm afraid for now it's two other manuscripts.

One of these is the educational research I've been referring to as "the homework project". It's been on the back burner while the graders we hired scored the quality of students' writing on various bits of coursework and the final exam. I think this is all finished now, though I don't even know where the data is. The teaching-research post-doc who was working closely with me on this project has started her new job back east, but she'll continue to be involved in the data analysis and writing. I'm also blessed with involvement of a new teaching-research post-doc, who'll be working with me here. (Both post-docs are part of our CWSEI program, not part of my own group.) The first step to getting the analysis and manuscript-writing under way is to email both of them and get the work organized. I'll do that this morning.

The other manuscript is the project I've been referring to as "USS-Perl". The basic computer simulation model now works well, our programming assistant has gone on to other things, and the post-doc involved with this project has done a lot of runs of the simulation to pin down some basic relationships between parameter settings and result. (I forget what these are, so I need to talk to her today about this.) I have a plan for the first manuscript, which I'll spell out in a separate post later today.