Well, I crashed and burned big time last week and let Anthony down.  My apologies, Ugh.  I still think we can revise and submit the shotgun DNA mapping paper, but the timing is not as urgent.  Thus, I am more tempted to port the code to something useful for the public.  Python (with it’s bio library) is what I’m thinking.  Mulling this over.  In the meantime, after many attempts, I finally got the github project going:

https://github.com/stevekochscience/Shotgun-DNA-Mapping–Yeast

It took forever, I think because it’s a huge library.  But it should include most of the sequences and simulations that Larry used for the first draft of the paper.

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I determined that the whitespace bug is indeed a problem in Larry’s code.  At least the code I’ve found.  In the VI, “initizing sub.vi” it definitely finds zero energies for the \n\r whitespaces.  As far as I can tell, this is not accounted for in the subsequent code.  I will test by using two different sequences and simulating with and without whitespace.  I don’t think this is (was) a problem, though, because the sequences Larry used didn’t have whitespace, I don’t think (at least after he found the XhoI sites)

-> Verified that the whitespace bug exists in “failed simulator again.vi”  to reiterate, though, this probably didn’t affect simulations, since the xhoi sites didn’t have whitespace after he found the sites

data files: Test 2012 pBR_2.dat and Test 2012 pBR_2no.dat (should be in github soon)