Important
Bioinformatics methods sections should convey the same level of information as a wet-lab methods section. They should be:
- clear
- reproducible
- adequately cite the tools used
Caution
Be careful if using a published paper as a template for your own methods section. Many published papers do not include sufficient information in their bioinformatics sections to be reproducible, and make for bad examples.
- Annotated example of how to write a methods section - An example of a generally good methods section and some key points where it might be improved - LP
1 Tips for Writing a Great Methods Section
- Describe your experimental methods in enough detail that your reader could replicate the experiments.
- Your methods section is not a protocol (a step-by-step list of everything that was done.) You may assume that your reader is a competent scientist with the skills to perform basic lab calculations, techniques, etc.
- Cite the appropriate literature (i.e. for any recipes, tools including software, and protocols you have used).
- Do not include results or rationale for performing experiments (these belong elsewhere in your thesis).
- Be clear and concise; eliminate unnecessary words and steps.
- Make sure that your methods section includes all of the materials and methods you used in your thesis (This includes any bioinformatics methods such as BLAST!)
- Ask a friend or colleague to read your methods section and give feedback.
Tip
Look at papers that have used similar methods: how are these methods sections written? Though take care as many papers underdescribe bioinformatics methods.
You want to make sure that your methods section generally follows the conventions in your field, so that readers will be able to understand it more easily.
A few examples of specific conventions:
- for wet-lab projects, centrifuge speeds are always given in xg, not in rpm or rcf
- for science communication projects, the design of your intervention/survey belongs in the methods section
- for bioinformatics projects, always include the version number and citation for any software used and details of parameters, etc.