Orientation

One of our goals for 2024 is to develop orientation materials for new students, postdocs, etc. There was broad interest in having a checklist, and example workflows for people to follow — particularly for projects that involve some form of code "hand over", to ensure that the recipients experience few problems in running the code themselves.

How to contribute

To suggest a new topic:

• Use the search box (top of the page) and check if the topic already exists;

• If the topic does not exist, submit a "New Topic" issue.

To suggest a useful resource: submit a "Useful Resource" issue.

To provide feedback about existing content: submit a "Feedback" issue.

To contribute new content:

• Use the search box (top of the page) and check if similar content already exists;

• If there is no similar content, please create a fork of this repository, add your contributions, and create a pull request.

• See our How to contribute page for more details, such as formatting guidelines.

Current issues for the orientation guide are listed here.

Suggested topics included:

• How to set up common tools on your laptop (e.g., Python and R);
• How to define a workflow and organise your files;
• How to write Markdown documents (see Nick Tierney's book RMarkdown for Scientists);
• How to format and check your code;
• How to set up git on your own device and using platforms such as GitHub;
• How to recover old versions of files;
• How to make your code device-agnostic, so it can run on HPC platforms, virtual machines, and can easily be migrated to new devices; and
• How to plan for reproducibility from the beginning, rather than waiting until you're preparing a publication.

Note

In addition to the topical guides, the Useful resources section includes:

• A beginner's guide to conducting reproducible research;
• A quick guide to organising computational biology projects;
• Examples of making models publicly available; and
• Examples of using GitHub Actions for Python and for R.