Introduction

This book is an attempt to centralize documentation and resources that might be useful to people working with the CAFRI lab. We have a number of pieces of documentation scattered across Slack, GitHub, Google Drive, and various websites, and this project aims to synthesize them into a more easily findable book.

That said, this is still an extremely new project. If you have any ideas for improvements – either editing existing content or adding entirely new documentation – please feel free to open an issue or contribute directly! The goal is for this book to contain every resource that’s useful for CAFRI folks – if you’ve ever had to answer the same question twice, you should write down the answer and add it to this book.

Using This Book

This book is publicly accessible from the internet, however we do not intend for this to be a public resource. Please do not send links to this material to people not in the CAFRI lab group. At the same time, please keep in mind that material included here might not stay within the lab – any private information or data should either not be included or should link to a more restricted resource.

Right now, the book is composed of four (ish) main sections, where most documentation should live:

• Joining the CAFRI Team contains most of the “general purpose” resources that are broadly applicable to most people joining the lab. Things about ESF, programming, and common hurdles for people live here.
• Standard Operating Procedures contains documents that are useful to everyone in the lab, no matter how long they’ve been around for. Specific technical resources, how-tos, and solutions to common problems live here.
• Ongoing Projects contains information that will be useful for anyone trying to get up to speed quickly on a specific project. We’ve also got a section for Completed Projects in case anything that was written is still useful.
• Everything Else contains, well, everything else. More specific documentation, including things that you wrote down “just for you” should live in here. Nothing is too random or too small for inclusion. Things that you’re linking people to frequently should probably live in a different section.

These sections are not set in stone – please feel free to make new sections and move things around if the current layout is not particularly useful.

Contributing

This book lives on GitHub, and is written using Quarto, which makes it easy to include code chunks in documentation.

Quarto books are written using Markdown, a plain text format that is designed to be easy to write and easy to read. The book is then automatically re-rendered every time we make changes.

That means that you don’t need to know anything other than some Markdown basics to make changes to this book. If you aren’t comfortable making changes directly, you can always open an issue on the book’s repo. More instructions on how to add to this book are in the contributing chapter.

A great first project, to get used to how we use git, GitHub, and this book, is to add yourself to the current members chapter!