I am just getting back up to speed with the code Larry wrote in 2009. This was before he became a bad-ass in LabVIEW, so the code is tough to read. I think the VI I was looking at yesterday was the wrong VI. I believe (now) the final VI Larry used for simulation was probably this one (again not yet publicly available):
- \\Controller\users\herskowitz.larry\My Documents\Sequencing\automated unzipping simulator through yeast genome with ant seq shutting off network.vi
This was last modified on 7/29/2009 and looks like what I remember we may have used. If only we had open notebooks back then (and Larry took good notes–zing!) it’d be much easier to Google and find the right code.
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Found some important files here (not public yet):
- \\controller\pub\Sequences
- \\Controller\users\herskowitz.larry\My Documents\Analysis of Deviation
- \\Controller\users\herskowitz.larry\My Documents\Deviation Analysis
- \\Controller\users\herskowitz.larry\Desktop\Graph in Patent Data
- \\Controller\users\herskowitz.larry\Desktop\Unformatted chromosome from yeastgenome.org
- \\Controller\users\herskowitz.larry\My Documents\Downhill Simplex
- \\Controller\users\herskowitz.larry\My Documents\July backup
Maybe hints at Larry’s nearest neighbor work: \\Controller\users\herskowitz.larry\Desktop\Sim data
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Wow! I realized that I encouraged Larry to use Visual SourceSafe, and he actually did (for some/most things?). I found many files in our sourcesafe database–if these end up being the important VIs, I will add all of them to github in a “larry” project, I think.
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So, It looks like “failed simulator again.vi” in Larry’s VSS is working properly. I compared a new simulation of pBR322 unzipping with a simulation from grad school, and they look very similar. Not exactly the same–possibly due to parameters, not sure yet.
4:35 PM: I opened up the old “Equilibrium model.vi” (from Jantzen) and the default values for GC/AT were 5 and 1.5. However, these values are clearly wrong with much too high of a force. At this point, I’m not sure how to figure out the values I used to create the 2002-ish file “pBR322 unzip 2002 calculated.dat”