Gas station without pumps

2011 December 2

I made it through National Blog Posting Month again

Filed under: Uncategorized — gasstationwithoutpumps @ 17:19
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At the beginning of November, I committed to writing a blog post a day for National Blog Posting Month (NaBloPoMo), an exercise that has gotten many people to post more to blogs.  Whether getting more people to blog is a good thing or not depends on how much you value blogs—I find that a lot of my time is now wasted reading many blogs, though I occasionally pick up a useful or interesting nugget of information.

I managed once again to write a post a day, mainly by working in bursts, queuing up four or five posts to trickle out one a day. I still have over 100 draft posts to write, as new prompts for posts arrive at an average rate of about one a day.  Some of them will get stale before I get around to writing anything on them, and some (like my unwritten research papers) will sit around forever reproaching me for not tackling them.  My readership for November 2011 was not bad (5800 views), but not my record monthly readership.

As I wrote last year in Writer’s Block, reducing my barriers to getting stuff written was part of my reason for starting a blog, and last November when I joined NaBloPoMo, I said “If I make it through November at a post a day, I can try to dedicate December to getting out some of my research papers that are long overdue for publication.” That didn’t work last year, but let’s see if I can do better this year.

A lot of my more recent work is waiting for collaborators to finish wet-lab validation (the banana slug Ariolimax dolichophallus mitochondrial genome, the Vibrio cholerae genome, the Helicobacter pylori genome), while slightly older stuff is waiting for collaborators to have time to do some of the writing (the Pyrobaculum oguniense genome).  The really ancient stuff is mostly protein-structure prediction stuff (the scoring function for disulfides, scoring hydrogen bonds without explicit hydrogens, conformation change operators in undertaker, …) and I really have a hard time getting up any enthusiasm for it.  The disulfide paper has been written for 2 years, and I still haven’t submitted it—perhaps I should remove the courtesy co-author who added some delays and submit it to some minor journal.

I did this month get some PCR data on the Vibrio cholerae genome, confirming some of the things I was worried about in the first assembly.  I redid the assembly using a slightly different method, and got a dozen or so major differences, so I’m having to request some more PCR to see which of the assembly techniques is more accurate.  Both were using the same 454 data (plus some Sanger sequencing of PCR reactions for the second assembly, but they made no difference).  The big difference was in whether I did a mapping assembly (using a previously sequenced strain of Vibrio cholerae), or did a de novo assembly and ordered and oriented the contigs by mapping to the previous assembly.  With the mapping assembly, I had fewer differences from the reference genome, but I don’t know whether this is because the de novo assembly failed to assemble some parts or if the mapping assembly copied parts of the reference for which there was really insufficient data.  A lot of the changes were in repeat regions (like the ribosomal operon) that could easily have degraded in some copies, so there is no way that I can tell which assembly is right, other than by having PCR reactions done to look at the length or the sequence of DNA between distinctive primers. It feels good to have gotten some productive work done, even if not written up.

Other productive work this quarter includes the improved velocity and acceleration extraction in Tracker (which I probably won’t write up other than in my blog, unless someone can recommend a journal for which it is appropriate—and not an author-pays journal).

I have gotten the ghmm package working on my laptop again (it had been broken by the installation of Vpython—Vpython insists on 32-bit Python, but ghmm compiles only for 64-bit Python on a 64-bit architecture), so I can get back to work on the HMM analysis of nanopore current data again.  If I get something working there, I can probably get a co-authored paper out with the nanopore people who generate the data.

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