The Bio-protocol experience

A few months ago, I joined Bio-protocol as an associate editor. The first  protocol I edited is now published, so I thought I’ll write about this experience.


Bio-protocol is an open access, peer-reviewed e-journal which specializes, you guessed it, in publishing life-science protocols. Submission is almost exclusively by formal invitation and it is free of charge (i.e. no submission or publishing fees).

I first heard about Bio-protocol at last year’s ASCB meeting. There I’ve learned that it was established in 2011 by a group of Stanford researchers. Also, to cite from the website:

“Our mission is to make life science research more efficient and reproducible by curating and hosting high quality, open access, life science protocols.”

I thought this was a good cause, so I joined as a reviewer. I also offered my help as an editor, for two reasons. First, I noticed there was no cell biology/molecular biology editor at the time. Second, I thought it  will be a good experience for me. After my first review (for a protocol that was written terribly), I was accepted as associate editor.

A few more details about Bio-protocol, which just celebrated 5 years:

  • There are currently ~1400 protocols published, which are organized by field (11 fields) and organism (10 groups). These come from researchers all over the world (but mostly US & Europe. See map below).
  • The annual number of users rose from ~50,000 in 2012 to about 400,000 in 2015.
  • The team includes 4 executive editors, 10 advisers, 58 associate editors and >400 listed reviewers.

author_mapOur goal is to publish detailed step-by-step protocols that can be followed easily by experts and non-experts in the field. Protocols are typically accompanied by illustrations to facilitate understanding of the process;  examples of expected results and how to interpret them; and sometimes video of specific steps in the protocol.

We are also proud to announce that we are now partners of elife

“…we would encourage authors to also consider submitting a detailed protocol to Bio-protocol…” Quoted lines from eLife.

So how does the process work?

The associate editors (such as myself) read research papers and recommend protocols from within the Methods sections. We need to make sure there are no similar (or identical) protocols already published or in-process with Bio-protocol. Also, we try not to publish protocols that were already published in other peer-reviewed methods journals (such as Nature methods, Nature protocols, Methods in Enzymology etc…).

I typically browse through recent papers of the last few months. We generally do not go for papers older than a couple of years. The reason is that by this time the student that developed that protocol has probably left the lab. So unless the lab continues to use this protocol (& publish), it is unlikely that the PI will agree to write & send us the detailed protocol.

Authors can also recommend their own protocols by filling in our pre-submission form.

Next, our exec editor sends the invitations to the 1st & last authors. Unfortunately, very few authors accept our invitations.

Once an author accepts our invitation, we register the protocol (so no similar protocols are invited).

Then we wait (we ask for submission within two months).

Submission is easy, since we do not have any restrictions on format, length, etc… We just require the protocol to be as detailed as possible.

Once submitted, it is assigned (by me) to appropriate categories (field, organism, type of method), re-formatted (by the team) and then I need to assign reviewers.

This is a rather tiresome process, since one needs to sort through our multitude of reviewers to find such that are suitable; send invitations; and hope the reviewers accept the invitation. I only needed two reviewers (I’m the 3rd reviewer). But I had to invite 7 to get 2.

For that first paper, the review process was not long. It took several days to find the reviewers, but once accepted, they sent their review within less than 2 weeks (we give them 18 days).  The authors also responded quickly so from submission to “accepted” took about one & a half months.

We ask the reviewers to concentrate on reproducibility and clarity of the protocol. Does it contain details on all of the reagents? Is it clear what happens at each step? Will the protocol be improved by adding more text/figure/video?

Remember that this protocol was already peer-reviewed, and published as part of a scientific publication, so we consider that to be a good sign that this protocol is working and have scientific utility.

Of course, if the protocol contains some illogical or improbable steps, one should not ignore that…

Once all three reviewers submit their comments, I make sure their comments are logical and clear, then send to the authors. Once a revised version is submitted, we, the reviewers make sure it is OK. If everything is fine, the protocol is accepted.

So, that’s about it. To me, the most time consuming step is the first step of recommending protocols. The most interesting was reviewing the protocol, comparing that to the protocol published in the original research paper, and comparing my comments to those of the other reviewers.

So far, I only went through it for one protocol. Another was just submitted and several invitations were accepted, but not submitted yet.


After a protocol is published – it’s not done. Readers can post questions to authors to troubleshoot experiments. Readers can also post reproducibility feedback – did the protocol work as expected? Authors can edit their protocol based on such comments.

So, if you’ve read thus far you are probably interested, so you are invited to be a reader, be a reviewer or be an author at Bio-protocol.



13 responses to “The Bio-protocol experience

  1. Are you still a reviewer for this journal? Any updates on how you see this journal? I have an interest in publishing it but the visibility is not that good (as far as I can judge, seems not to be automatically added to NCBI, pubmed).


    • Hi, I am an assoc. editor at bio protocol. Pubmed is a sore spot – it took a long time and lots of beaurocracy to get approved into their system. Now that we are, protocols will appear there. As for visibility, we have over 2000 protocols already and had 2 million visitors last year. We partnered with eLife, JCB, bioRxiv and several other journals. They also refer to us. And we are constantly growing.


      • Ah I am glad to read this. I personally do not really care about the visibility in pubmed, but others (with which I work) do care about it. I actually like the journal and set up and would like to publish in it, but too many people still focus on “visibility in pubmed” and impact factor. Does the journal actually have an impact factor?


        • I don’t think BP has an impact factor. In any case, BP only publishes protocols from already published papers. more important – unlike other journals like nature protocols it is open access to readers, and unlike JOVE it is also free to publish – no fee from authors.


          • This might be a problem for me as I want to publish a method that has not yet (at least not as what I did) been published in other papers. This is actually my problem: I have a method (and results) but want to publish the method at the moment without giving away the results yet because I can use them to get a paper in a vey high impact journal (but need some extra work for it). So I am looking for a journal that lets me publish a method that has not yet (completely) been published without results.


          • just got updated by our executive editor on our pubmed status:
            As for PubMed indexing, currently there is a subset of our authors – those with funding from NIH and a subset ofother US funding agencies (see for details) or Europe PMC Funders Group ( — are permitted to submit their accepted papers for inclusion in PMC. If author’s funding does not come from any of these sources, their protocol will not be able to be included in PMC.

            We applied for full inclusion of Bio-protocol in PMC last Nov. and will get the result in ~6 weeks.


          • Oh ok, thanks. It is a bit strange that the journal is not , fully, included on PubMed since it is the biggest (as far as I know) one for protocol type papers. Do you know if they will get an impact factor as well? Or the citation number is too low ? Kinda curious because protocols are so important that I always wonder why people somehow never refer to them.


          • As far as I uderstand, inclusion in pubmed is notautomatic. Any journal that wants to be included needs go through a review comittee and there are certain guidelines & requirements. See here for details:


          • Well I do hope it gets accepted!
            I pretty much finished writing my protocol. I hope I can somehow publish it in the journal, it would make my life a lot easier and also those that want to re-do the protocol.
            Now I just need to finish the paper that goes with the protocol. I am actually referring in that paper to the protocol, so I hope to be able to publish the protocol first.


  2. We also accept protocols from pre-prints, so if you post your paper as a pre-print you can already send us a pre-submission inquiry.


    • yeah; I’ll have to look into it when I finished my other paper. If all goes well and my PI agrees with me publishing the protocol right before the other paper, I’ll for sure publish the protocol first. But I have to time it so it is not published too soon as well.
      What exactly is a pre-submission inquiry?


      • Typically we invite authors by our editorial team or editors of collaborating journals. But authors can ask to be invited by a pre submission inquiry
        Regarding preprints we will time the publication of the protocol to occur together with the reasearch paper. Or at least once it is accepted and has a publication date.


        • Ok, good to know. I think I need it published a bit before the other paper because I referring in the other paper to that protocol…
          (but I have to figure this all out with my PI and hear what he has to say).
          Thanks for the information, I’ll keep it in mind and hopefully not long from now I can start the processes of getting it all published.


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