One big protocol or lots of little protocols



I work in molecular biology, and I often use multiple “protocols” to perform a single experiment. I was curious if other people on here prefer to format their experiments as one large multi step protocol or run a series of smaller protocols. I think smaller protocols that I can start and finish with the larger experiment in mind is easier for me to schedule tasks.

I haven’t tried out the link function, but I think it might be my next step. Creating and Using Links

Any comments or suggestions?



When I worked on Findings 1, the idea of multiple protocols per experiment was very much in my mind and guided quite a few of the development decisions. While protocols have been de-emphasized to make their use optional, when you use them, they are meant to provide exactly the flexibility you describe. By inserting a protocol into an experiment, you create a copy that you can alter if needed, and where you can mark things as done or add timestamps.


In my case it depends on the experiment I’m doing. I like to have protocols as blocks that are always done as one.

A western blot, for example, would be one protocol, as I always try to do it from lysis to revealing. An immunostaining will also be only one protocol. I have 3 different immunostaining protocols depending on the kind of sample I have.

A cloning, in the other hand is split in few protocols: DNA digestion, dephosphorylation, PCR, electrophoresis, ligation and transformation. Depending which cloning I do, I just add the protocols needed. Otherwise I’d need to do a protocol for each kind of cloning, with all of them sharing certain steps (transformation) and with variations on the intermediate steps.

This way, I have a lot of flexibility to put various protocols as if they were pieces of a puzzle, or just one protocol if it always follows the same number of steps.



I tried out inserting protocols into ongoing experiments, and I can see the functionality of it. I include a lot of the additional details currently in “day 0” of all my experiments even though its not technically done the day before I start. This can cause the insertion to not work out perfectly, but its easy enough make modifications. I like the ability to be finished with certain portions to keep track of what I have finished in various protocols though.

Thats interesting Pablo, I think thats an excellent way of explaining how I break mine up as well. I know a lot of different protocols of mine share many characteristics, and I like to drop in the “version” of DNA extraction that I need to do for one versus the other.