Suppose a professor or student at a university uses software like Rosetta (a protein folding software) for their research. Rosetta has free academic licenses as well as paid commercial licenses available. The professor or student uses an academic license for their research.
Now, suppose eventually that professor or student discovers a new technology (e.g. they design a new medically useful drug using Rosetta). Is the professor or student allowed to patent their discovery and license that patent (or start a company that uses it)?
In other words, does the use of the non-commercial software license mean that any technologies developed using that software couldn't be monetized? Or does it just mean that nobody working for a commercial organization can use the software (a weaker constraint)? If the latter case, what would prevent companies from using small nonprofit proxy organizations to do research under the noncommercial license, only to then patent and transfer the patented technology to the main company?