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.
Found some important files here (not public yet):
- \\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
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.
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”