An Exchange of Views

Go to the profile of Chris Surridge
Dec 01, 2010
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It’s the first of December so let’s open the first window of the protocols advent calendar. And behind it we find a very pleasant surprise. All shiny and new, a free and open web resource for the sharing of protocols across the scientific community. And the name of this wonder is:

Protocol Exchange.jpg

I confess this isn’t so much of a surprise to those of us who have been working on the project for a year or more. It’s serendipitous that it is live today but we knew that it was coming. Strictly speaking it isn’t even a new idea either. Nature Protocols has been allowing authors to upload their protocols onto a section of the website called Protocols Network. However that site was a little low on functionality, so we now bring you a gleaming new site, explicitly for the exchange of methodological know-how.

Why is this important?

Science doesn’t progress by results alone. Essentially the same experiments are employed again and again by different researchers to explore similar but different questions. More than that no result in science can be trusted unless it can be reproduced, and for someone else to repeat an experiment they need to know exactly what was done. In research papers there are methods sections but they are often less detailed than one would wish. As helpful as a restaurant review when you are trying to cook a romantic meal. What you really need is a tried and tested recipe. Of course that is what Nature Protocols brings you but no journal can publish how every experiment is done in every lab in the world. Nature Protocols tries to bring you the gold standard procedures, peer reviewed and professionally presented. But there is a wealth of experimental know-how that is locked up in the personal manuals of laboratories only accessible to people working in those labs. In these hyper-connected times we must be able to do better; unlock that knowledge to make setting up new experiments easier and research as a whole more reproducible. That is where Protocol Exchange comes in.

There is a great deal to tell you about Protocol Exchange perhaps enough to take up all the windows on our advent calendar, or at least enough for a Twelve days of ProtEx-mas (other winter festivals are available). For now let’s start with the basics.

What can you find in Protocol Exchange?

home page.jpg

Well protocols obviously. Researchers can upload their protocols to Protocol Exchange through a simple and intuitive series of pages. There are fields for introduction, materials, anticipated results, figures, tables, in fact most of the things that go into the Nature Protocols format. Most of them aren’t obligatory but if you do take the time to fill them in the result is a beautifully styled protocol, easy to read and navigate. Sharing a protocol on Protocol Exchange costs nothing. Reading a protocol costs nothing. Indeed all the protocols are presented under a Creative Commons Attribution-Noncommercial licence which allows for unrestricted copying and reuse of the protocol as long as the source if properly credited and the reuse is not for commercial purposes.

Connected to protocols are the research papers in which they are used. Protocol Exchange captures that information too. When sharing a protocol the authors can identify any research papers in which the protocol has been used or which is in some other way related to the protocol. All we need is the DOI of those papers and Protocol Exchange will create a page with citation and other information about the paper under which is a list of all the protocols that we have related to those papers. And of course a direct link to the research paper wherever it is published.

Three legged stools are the most stable and Protocol Exchange third leg is the people who create the protocols. Not individual authors so much as the Lab Groups in which the protocol was developed. Every protocol in Protocol Exchange has an associated Lab Group. Anybody can create a Lab Group and then invite other researchers to join. Or the Group can accept applications for membership. Or the Group can be set open so that anyone can join straight away. A little bit of social networking the reflect the way that scientists collaborate to invent and evolve ways of doing science.

We expect that Lab Groups will be used as the name suggests. A researcher will set up a group and invite all the other people in their lab. Then all the Protocols from that lab, whoever actually writes them, can be collected together. Lab Groups have their own personal page which lists all the Protocols from that group. A picture can be uploaded to be the logo of the Group, a link to the personal or departmental website can be added and other information about the Group if desired. All members of a Lab Group can see any of the Protocols being drafted by other members of the Group before they are officially shared, giving them the opportunity to offer constructive advice to their colleagues. There is much more to be said about Lab Groups as I think there are some subtle and powerful ways that they can be used, but that is for another day.

Come and have a look at Protocol Exchange. I really believe that this could be a major tool for scientists striving for reproducibility. As we have moved all the protocols from the old Protocols Network into Protocol Exchange there is already plenty to look at.

Best practice isn’t something that can be achieved in isolation, Nature Protocols and Protocol Exchange are where best practice can be spread around.

Next time: Two Turtle Doves!

Go to the profile of Chris Surridge

Chris Surridge

Chief Editor, Nature Plants

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