Q: How do we describe the use of software in the Materials and Methods section of a dissertation?

Generally, in the Materials and Methods section (or simply, the Methods section) of a research paper, it is important to include sufficient detail about all materials, equipment, and software used to ensure reproducibility (as you can read in this article: Supply adequate details of items mentioned in the materials and methods section) Readers should be able to understand and replicate what you did, validate what you did, and be able to use your approach.

Coming to your question, the answer would depend on the focus of the research. Does the software used in your study directly impact the results? Examples of such studies would be in computational fields, involving numerical modelling, simulations, performance evaluations of algorithms, etc. If so, all parameters and inputs might need to be described. If the data are too voluminous, additional details might even be supplied as supplementary material.

However, if you have used software for analyzing data that has been collected or generated by you, you may simply indicate the module or specific packages, subroutines, queries, etc., used, along with the version of the software and developer/publisher details. Consider for instance an ecology paper dealing with species richness. In the relevant subsection of the Methods section, you might mention that you used the vegan package of the software R and specify the version and author/publisher of the software.

To reiterate, the level of detail of the software and related parameters to be described would depend on the nature of the study. Irrespective of the field of study, however, it is critical that the software used be acknowledged in the main text and/or references, with complete details of the source.

For more help with the key points discussed above, you may find the following resources useful:

• How to write the Methods section of a research paper
• Getting the references right: citing books as a source of information
• What is meant by 'Code availability (software application or custom code)' during submission?

Hope that helps. All the best for your dissertation!