Little steps

The purR knockout cells grew on the kanamycin agar, and I purified DNA from them. Today I'll grow up the hypercompetent mutants, give them some of the DNA, and plate them on kanamycin. These mutants are so competent that I won't need to starve them, and I don't even need to bother measuring the DNA concentration before I use it. If nothing goes wrong, tomorrow I should have my mutants.

Of course something usually does go wrong:

"Most scientists spend most of their time trying to figure out why their experiments won't work."

R. Redfield

I spent most of the weekend on the motif-search program, alternately testing the effects of different inputs and trying to understand the brief manual. The 'read-me' included a list of input 'flags' that would change the program settings, but this was very terse and I alternated between discovering that I had the flag format wrong and suspecting that the flag was being ignored. The manual is quite dense with information. I've made about eight attempts to read it, each time making sense of a few more points, but I still feel a bit too ignorant/confused to be able to ask the authors sensible questions by email.