An abbreviation is any shortened form of a word or phrase: “HEPES,” “Ph.D.,” “etc.,” etc.
Initialisms comprise a subset of abbreviations where the first letter of each word (more or less) of a phrase are combined. Some examples include the “Food and Drug Administration” = “FDA,” “adenosine di-phosphate” = “ADP”, and “4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid” = “HEPES.”
In physical science manuscripts, nearly all initialisms should be written in all capital letters without spaces or periods. (There are some exceptions, such as “a.m.,” “r.m.s.d.,” etc.) This is certainly the case if you introduce new initialisms for brevity or clarity. When introducing an initialism, write it out first, followed by the abbrevation in parentheses: e.g. “structural genomics (SG).” Don’t underline or otherwise highlight the letters used in the initialism.* Don’t introduce new or uncommon initialisms unless you will be using the term several times.
Technically, not all initialisms are acronyms, even though in common spoken English the terms are largely used interchangeably. Acronyms comprise the subset of initialisms that are pronounced as a word rather than a spelled list of letters. For example, “AIDS” and “laser” are acronyms, while “ADP” and “NIH” are initialisms.
* Yes, I know I did that in the prior paragraph. Hey! What’s that over there! <runs away>