matsengrp / torchdms

Analyze deep mutational scanning data with PyTorch
https://matsengrp.github.io/torchdms/
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Will's edits to paper #162

Closed wsdewitt closed 2 years ago

wsdewitt commented 2 years ago

My edits to the paper. These are mostly minor, but one more significant change is I removed most reference to "fitness" or "fitness landscape", replacing with "function/phenotype" and "genotype-phenotype map". Protein researchers often equate protein fitness to function, so this is sort of a normal thing to do, but it is pretty confusing: proteins don't have fitness in an evolutionary sense, an organism (virus) has a fitness that depends on protein function. Since we are also interested in modeling actual evolutionary fitness as a function of protein function (e.g. in GCreplay), this is especially problematic. The flow is genotype-->phenotype-->fitness, and torchdms is only about the first link.

Feel free to accept/reject changes as you see fit.