From PhD thesis to Protocol Exchange

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

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.


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.