Friday, June 26, 2009

Plan for the next few weeks

One proposal down, one to go... The next one isn’t due until August 8th, so I’ve got just over a month to get it done. This time, however, I am going to manage my time better, since I need to get some preliminary data and still keep learning how to use a computer.

So here’s my plan for the next several weeks:

(1) Work on the proposal for a limited time each day (~1-2 hrs). I’ll start by developing a detailed outline of what I want to say and the order I want to say it, rather than leaping straight into writing. Based on my experience with this last one and in the past, I find I am an extremely inefficient writer (both with my time and with my words), so hopefully I can improve by having more focused daily goals.

(2) Work on the computational stuff only 1-2 hrs per day. Still need to fix the browser to display the Hin genome. Still want to work out the best way to align the genomes and report differences... particularly enumerating structural variation (non-SNPs). I also need to keep a mind towards what file formats I expect to get from sequencing. It might be particularly useful to try and simulate the kinds of results I might expect from sequencing periplasmic uptake DNA, etc.

(3) The rest of the time will be dedicated to lab work. The priority is to use defined fragments (USS-1 and USS-R) to work out a periplasmic DNA purification protocol. I’ve got cleaned amplified USS-1 and USS-R fragments, and I’m making competent cells of wild-type and rec-2 today. I tried to grow up a pilA mutant to use as a no uptake control, but something was wonky with the strain. All I need now is label. And a calibrated Geiger counter. I’ll get these things done today.

(The image above was made using the Mac-specific application GenomeMatcher. It represents a BLAST alignment between KW20 and 086-28NP across an interval containing several inversions. It also has a bunch of useful-seeming utilities that I'd like to figure out. Now if I could just get it to use my MUMmer program, like it’s supposed to...)

1 comment:

  1. Your blog-post writing is very clear and well-organized. For me, something about the blog-writing process helps me organize my ideas, sentences and paragraphs so they're easy to follow. When I write for the formal goal of a writing task, I get bogged down, but if it's just a blog post then the words flow (well, not in this comment...). Later I take what I've written and polish it to satisfy the formal goal.