Bench to Byte: A biologist's guide to crafting quality code

I made this guide for biologists with moderate programming experience who want to improve the way they work. You'll learn how to organize your projects, use remote resources, create reproducible software environments, and build computational pipelines.

This guide was made with members of the Bloom lab in mind. In the future, I might expand this resource to apply to a more general audience.

Developing

To develop Bench to Byte, you'll need to set up a few things. Specifically, you'll need two pieces of software: Node.js and npm. Node.js is an environment that allows you to run Javascript code on your computer. npm is a package manager that handles the Javascript libraries necessary to create this website.

The instructions for installing Node and npm depend on your operating system and personal preference. For detailed instructions check out this website.

However, if you have conda installed, you can use conda to install node and npm using the environment.yml file in the repo.

conda env create -f environment.yml
conda activate bench-to-byte

Once Node and npm are installed, verify by running:

node -v
npm -v

You should see the node and npm versions that you installed on your system.

If this is the first time you're developing bench-to-byte, you'll need to install the packages in packages.json. To do this, run the following command from within the repository:

npm install

With everything installed, you can now boot up a live preview of the website that automatically reflects your changes upon saving.

npm run docs:dev

Now, there will be a local version of the website running at http://localhost:5173. Visit this URL in your browser to see a preview of the site.

Note, If you are developing bench-to-byte from a remote server (not your local machine), use

npm run remote:docs:dev

and access the preview at the URL provided under Network

Contributing

Bench to Byte is based on the static site generator VitePress. This allows you to create fully functional web pages using Markdown files. To add a new page to the site, you simply create a markdown document in the correct directory and make a pull request.

For more details on writing markdown for a Vitepress website, see the markdown reference here.

Project Structure

.
├── README.md
├── environment.yml
├── index.md
├── chapters
│   ├── chatgpt-and-llms
│   │   └── index.md
│   ├── coding-best-practices
│   │   └── index.md
│   ├── creating-workflows-and-pipelines
│   │   └── index.md
│   ├── introduction
│   │   └── index.md
│   ├── managing-software-environments
│   │   └── index.md
│   ├── organizing-your-projects
│   │   └── index.md
│   ├── setting-up-your-ide
│   │   └── index.md
│   ├── tracking-your-code
│   │   └── index.md
│   ├── using-remote-resources
│   │   └── index.md
│   └── working-collaboratively
│       └── index.md
├── package-lock.json
├── package.json
└── public
    └── logo.png

To add details to a specific chapter of the course, simply edit the index.md file under the corresponding chapters/<chapter-you-are-editing>/ directory. If you want to include images in your markdown, you can either use a link to a remotely hosted image or add the image to the public/ directory and reference it like so:

![Alt Text](/my-image.png)

If you've contributed in some way to this guide, add your name and a link to a photo in public/contributors.json.

Suggestions

If you have any suggestions for topics that aren't covered in this giude, please suggest them in the corresponding Discussions thread.