The minor snags with using the new server were easily resolved, and yesterday I queue'd up all of the runs needed for the data on mutation-rate effects. Some of them I queue'd up twice because I made mistakes in the settings the first time - one result of this is that we'll have five rather than four replicates of the key runs. And all but two of the runs had finished by this morning - the two still running were doing 50,000 cycles rather than 10,000.
The new writing plan is to generate a draft manuscript (very crude in spots) and draft figures (some in final form, a few just sketches because I don't have the final simulation data yet), and send the whole thing off to my co-author. She can then revise the draft while I generate and analyze the rest of the data and create the semi-final figures. Our goal is to have the semi-final version of the whole thing ready when we meet up at the Gordon Conference on Microbial Population Biology (end of July), and to do the final revisions together then.