There is Method to the Madness -The Basic Outline of a Scientific Paper, Part 2: The Method Section

This is always the most boring section to write. Sorry, I have no cure for that! However, you must keep in mind that there has to have enough information in the Methods so that someone could duplicate what you did. When I was in the laboratory, I regularly took a paper and worked a method up sufficiently to incorporate it into our work. Some papers were better than others at giving me enough information to do that. These days many journals put the Methods in the online supplemental section. Methods there can and should be more detailed. There is no excuse for incomplete methodology when it is in a supplement.

There are a few general rules to follow that should make the Methods section a bit easier to write (in no particular order):

1. Try to organize the methods in the same order as you used them to generate results. This will align the Methods section with the Results section and make it easier for the reader to understand what you did. And if you always did one assay or extraction before another, make sure that is the way they are ordered in the text.

2. Refer to the assay or method the same way in the text and the figure legends. Too often I have found the figure legends different than the text. Consistency is key, as you might have guessed from the number of times I use the word in my blogging!

3. Make sure that every method you used to generate results is discussed. I have seen methods given in figure legends that are not found in the text.

4. Some methods are included that generate reagents (e.g. transgenic mice). Make sure they are introduced before the methods that use the reagent are discussed.

5. If a kit or machine generates data (i.e. actually measures something for you), you must give the specific kit or model along with the manufacturer. Some methods cannot be duplicated with different source materials or machines.

6. If you are using a kit and following the manufacturer’s instructions, say that. Do not go over the steps, unless you changed something, and then be specific about what was changed and why.

7. If a method has already been published, then cite the reference. If there are no changes, this is acceptable without more detail. If some reagents, like antibodies, are different, then note that. However, if there are significant differences from the published method, you should go over the details.

8. If you are using an acronym for an assay or method (i.e. ELISA or NMR), be consistent, same for an assay with a name, like Western blot or immunoprecipitation. Use the same word to refer to the same thing.

9. Check the journal for whether abbreviations need to have periods after them—hr or hr. Most have eliminated the period.

10. Most of the time, once you have published a method, you can cite it or cut and paste sections.

Most methods can really only be written one way that allows them to be followed, so they always seem repetitious. But the details here matter, when in doubt put in more details.