10:45 AM: Found some more stuff in \\Controller\users\herskowitz.larry\My Documents

• This looks like stuff he used for analysis (matching) after simulation messing around has data in it.vi
• This has promise for being the program that finds the XhoI sequences: new formatting program.vi

Also, some locations of data files

• \\controller\pub\,dropzone\August 28 pCP681 files for Larry

Some simulation files

• \\controller\pub\8 and 8b Force Measurements

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Figured out something that was confusing me: The sequences around the recognition site for both upstream and downstream are stored in the same files in this directory: \\controller\pub\Sequences\Yeast Genome.  So, I think pretty confidently, these are where most of the sequences Larry simulated are.  A remaining question (that I will have to answer via looking at software (probably “new formatting program.vi”)) is whether he threw out sites that were too close to other sites.

-> Note: Github says as long as I keep each public repository under 1 GiB I should be OK on diskspace

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5:45 PM Still working on github, not sure if I’ll have time to upload tonight.  Git was being super-slow on LarryXP (maybe because I was using a networked folder).  Now copying to my laptop to upload later at home.  About half done in about an hour

Also, There is an important possible bug in Larry software (not sure yet, but definitely a misconception that I had).  He was using a Richard sub-VI called “Trim whitespace” (see picture below) that only removes whitespace from beginning and end of string.  I thought it worked on the whole string.