Protocols are generally understood as sets of rules. There are etiquette protocols, computer protocols, political protocols, and even laboratory protocols.
For biologists and bench scientists protocols are lab recipes followed to achieve a specific outcome. As there are many different recipes for chocolate chip cookies, there are different ways to culture epithelial cells, derive rat ES cells, and image action potentials.
Protocols are useful because they go into more detail than is generally given in the Methods section of a journal article. Researchers share their protocols between labs, but they also publish protocols as separate articles in journals or book series devoted to protocols.
Now these journals and book series are online databases that JHU researchers have access to and are listed in the Biological Sciences guide. Video is also being used to illustrate the steps involved in the protocols. SpringerProtocols, Current Protocols, and Nature Protocols have some video content. JoVE is a peer-reviewed video journal about lab procedures.
BTW, there are such things as biology cookies!
(1) This is great post, and protocols are indeed extremely important. (2) Please bring us some biology cookies.