methods.qmd

---
title: "Writing Bioinformatics Methods"
image: ./assets/images/methods.jpg
description: |
 Advice for writing bioinformatics methods
number-sections: true
about:
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html:
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---

::: {.callout-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
:::

::: {.callout-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](./assets/docs/methods_example.docx)  - _An example of a generally good methods section and some key points where it might be improved - LP_

## 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.

::: {.callout-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.