In the last week, we have pushed nine new protocols live on the Protocol Exchange. They were all uploaded by Wei Zou and are based on work that he did towards a PhD in nutritional biochemistry¹.

Conceptually, I think that extracting methods from the PhD thesis, converting to protocol format and publishing on-line is an excellent idea.

– The researcher is able to share the methods they have developed and optimised during the course of their PhD with a wider scientific community.

– If the appropriate references are prominently cited, this would likely increase traffic to related primary research articles.

There are added advantages of uploading them to a site like the Protocol Exchange, for example:

– The protocols would have a “home” that does not have to be maintained by the researcher or his/her institution (and would be “stationary” while the researchers may move from one laboratory to the next).

– The protocols are sorted by category and can be found using a search/browse faciltiy.

– Each protocol is indexed with CrossRef and assigned a DOI,and – in the case of Exchange Protocols – can found by searching via nature.com.

I acknowledge that there are some barriers to doing this. In the case of the Protocol Exchange, I think that the main ones are:

– Converting the text of the Procedure to the active tense (especially if the Procedure is quite long and/or is more discursive in nature).

– That it is not obvious how you would include in-text tables and figures (and equations) where these are necessary.

There are, however, some possibilities for making things easier:

You can, for example, upload a Word document or pdf so that the user can access a version including all (or parts) of the text so that it can be viewed or printed off with exactly the formatting that you would like².

In conclusion:

I think that it would be great if more people uploaded the methods from their theses as Exchange Protocols!

I would be very interested in your views on this. You could share these by either filling in the fields in the survey, writing a comment below, or dropping an email.

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¹ – Wei Zou is currently working at the California Department of Toxic Substances Control. The protocols mentioned above are based on work that he did towards a PhD in nutritional biochemistry (Carnitine and fatty acid metabolism, 2002) working with Sung Koo while both were at Kansas State University. These led to a primary article plus a patent. He then went on to do postdoctoral work on metabolomics under the supervision of Vladimir Tolstikov and group leader Professor Oliver Fiehn at UC Davis.

² – In the case of Extraction of Fatty Acids for Capillary Gas Chromatography Analysis, the section describing the GC methods contained a lot of tabulated information, and it made most sense to upload this as a Word document and a link to this document was included in the Procedure section.

– Bull and co-workers went all the way, and uploaded each section of their protocol as individual pdfs, plus a pdf for the protocol in its entirety. Organotypic explant culture of adult rat retina for in vitro investigations of neurodegeneration, neuroprotection and cell transplantation.