Sunday, March 20, 2016

My Experience Sharing Protocols in the New "" Environment

Scientists publish methods in their manuscripts, but these summaries can fail to capture the technical details involved in the described processes. Many scientists get around this by by making the actual step-by-step protocols freely available to the public. There are a variety of avenues for accomplishing this. Some scientists publish their protocols with their manuscripts, some post them in public archives, and others publish them on their lab websites. There are advantages and disadvantages to these approaches, and most of us are always learning about new and improved resources to facilitate the sharing process. I recently learned about the online resource, which is a surprisingly robust and free resource for sharing experimental protocols.

I originally learned about when their group VERVE Net (of the Hurwitz lab) graciously transcribed our group's published computational protocols over to the environment. Our computational protocols were originally archived on FigShare. Although the protocols were only recently uploaded to, I have been impressed with what it offers.

The most compelling benefit I can see with using is that it offers a new degree of visibility to your research. By being part of their environment, your protocols are searched for, and viewed by, a wider scientific audience. This means that more people will learn about your research, use the approaches you developed, and cite your work as a beneficial contribution to the field.

The other benefit I can see from using is the user-friendly interface optimized for scientific use. Not only can you search for and view protocols, but you can follow along with them in their app step-by-step, check off completed tasks, use integrated timers, etc. You can also fork protocols (i.e. make your own copy) that you can update to meet your own experimental needs. It definitely feels like it was influenced by common software version control resources such as Git.

Now this is all fine, but wouldn't a system like this only be good for "wet lab" protocols and not computational workflows? It certainly seems to have been built for "wet lab" protocols, but it works surprisingly well with computational workflows too. I honestly don't see it replacing source code repositories such as GitHub, but I do think it has a place for publishing widely-used standard operating procedures (SOPs) for various bioinformatics tasks. As an example, the Mothur SOP for processing 16S rRNA sequencing data is available on the Mothur Wiki as a step-by-step workflow. I could see a reference workflow like this being published in the environment.

So in the end, I would suggest checking out. It is a cool effort toward promotion of scientific transparency and collaboration, and I think you could benefit from using it.

Did I miss something or fail to elaborate on a point you want to hear more about? As always, I invite you to let me know in the comments below.  I would love to hear from you!

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