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.

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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.

bio-protocol-table

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.

 

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