re: What exactly do Pharmacists do?

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aren't you basically just following directions

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Pharmacists mostly just supervise and direct elements of compounding that are basically just following directions. They'll figure out how to perform more complicated procedures. There is a definite art to nonsterile (e.g., creams) compounding, and the bulk of pharmacy compounding is sterile compounding where things can go really badly if people frick up.

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Couldn't there be a software program that does this

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There are. They suck, and the overwhelming majority of interactions they flag are acknowledged and ignored by prescriber and pharmacist.