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First, you have to check with the publication. Did you assign all rights to the publication at time of the printing? Or did your non-profit retain rights? See HERE. Many publications request that you turn over the copyright to them at time of publication. So the publication may own the right, I am afraid.
Even if it does (or does not), it is not really possible to copyright a scientific protocol. This is much for the same reason that it is not possible to copyright a recipe: Copyright law does not protect recipes that are mere listings of ingredients. Nor does it protect other mere listings of ingredients such as those found in formulas, compounds, or prescriptions. While scientific protocol is a little more than that, it is in the end a list of steps/ingredients and thus, an attempt to copyright it is likely to fail (or a challenge to it).
Now NOTE: Copyright protection may, however, extend to substantial literary expression—a description, explanation, or illustration, for example—that accompanies a recipe or formula or to a combination of recipes, as in a cookbook. So an original publication by your non-profit which has a more involved piece than just steps/ingredients may be subject to copyright. That is assuming it is not being held already by the publication journal from 2015.
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