Trynka Lab website

The website is built with Rspress and published through GitHub Pages. Most contributors only need to add or edit Markdown files; they do not need to change React components, configuration, or build scripts.

Content contributor guide

Where to update content

Website section	Markdown to edit
About us	docs/about-us/index.md
Publications	One file per paper in publications/
Software overview	docs/software/index.md
sc-blipper documentation	software/sc-blipper/docs/v0.0.4-alpha/
tglow-pipeline documentation	software/tglow-pipeline/docs/v0.0.1-beta/
tglow-r documentation	software/tglow-r/docs/v0.1.22/
tglow-core documentation	software/tglow-core/docs/v0.1.4/
edit-quant documentation	software/edit-quant/docs/v0.0.1/
ProliferationAnalysis documentation	software/proliferation-analysis/docs/v0.1.3/

The homepage banner and research placeholders are currently part of the site layout. Ask a maintainer to change those rather than editing files under theme/. The About us navigation link currently opens the Trynka Group page on the Sanger website; docs/about-us/index.md is the local page reserved for future content.

Update an existing page

Open the corresponding .md file and edit its Markdown body. If the file has a frontmatter block between --- lines, keep that block at the top:

---
title: About us
---

Add or update the page text here.

## Research focus

Use normal Markdown for headings, links, lists, images, and code examples.

For software documentation, modify files only inside the current version folder. Existing filenames map directly to website pages, for example:

software/sc-blipper/docs/v0.0.4-alpha/installation.md
software/tglow-pipeline/docs/v0.0.1-beta/running.md

Add a software documentation page

Create a lowercase, hyphenated Markdown filename in the applicable current version folder:

software/<tool>/docs/<current-version>/new-page.md

Start the file with a descriptive heading and write the content in ordinary Markdown:

# New page title

Briefly explain what this page covers.

## First task

Add the instructions here.

Submit only the Markdown page. A maintainer can add it to the ordered sidebar when reviewing the contribution.

Add a publication

Create one Markdown file in publications/, named with the year and a short paper identifier, for example 2026-tglow.md:

---
title: "Paper title"
authors:
  - "First Author"
  - "Second Author"
year: 2026
date: "2026-02-11"
type: preprint
venue: "bioRxiv"
citation: "2026.02.10.704860"
doi: "10.64898/2026.02.10.704860"
url: "https://doi.org/10.64898/2026.02.10.704860"
codeUrl: "https://github.com/TrynkaLab/example"
---

One short summary paragraph shown on the Publications page.

Required fields are title, authors, year, date, type, venue, and url. type must be article or preprint, and date must use YYYY-MM-DD. citation, doi, and codeUrl are optional.

The website validates and sorts publication records automatically. Do not edit theme/generated/; it is recreated from the Markdown files during every development and production build. More details are available in publications/README.md.

Add images or downloads

• Put shared website assets in docs/public/.

• Put tool-specific images beside the relevant versioned Markdown page.

• Use lowercase, descriptive filenames without spaces.

• Reference a shared asset from Markdown with its public path:

  ![Description of the image](/images/example.png)

Submit a content change

1. Create a branch or edit the file through the GitHub web interface.
2. Add or modify only the relevant Markdown and image files.
3. Open a pull request targeting staging.
4. After review, a maintainer merges it into staging.
5. Review the deployed result at https://trynkalab.github.io/preview/.
6. A maintainer promotes the approved change to main for the official site.

Content contributors do not need to install Node.js or run the website locally; GitHub Actions builds the preview after approved changes reach staging.

Files content contributors should not edit

These contain implementation or generated output and are maintained separately:

theme/
scripts/
rspress.config.ts
software/software-config.ts
package.json
package-lock.json
doc_build/
node_modules/

Maintainer reference

Deployment environments

Branch	Purpose	Published path
main	Official website	/
staging	Preview and acceptance testing	/preview/

The deployment workflow is defined in .github/workflows/pages.yml. In Settings → Pages → Build and deployment, keep Source set to GitHub Actions.

The workflow builds main for https://trynkalab.github.io/ and places the staging build under https://trynkalab.github.io/preview/. Forks are detected automatically and receive the repository-name path prefix.

Repository structure

.
├── docs/                         # Main Trynka Lab website pages
│   ├── index.md                  # Homepage route
│   ├── about-us/index.md
│   ├── publications/index.mdx    # Publications page shell
│   ├── software/index.md
│   └── public/                   # Shared static assets
├── publications/                 # One Markdown record per paper
├── software/
│   ├── software-config.ts        # Tool metadata and version registry
│   ├── sc-blipper/docs/          # Versioned sc-blipper Markdown
│   ├── tglow-pipeline/docs/      # Versioned tglow-pipeline Markdown
│   ├── tglow-r/docs/             # Versioned tglow-r Markdown
│   ├── tglow-core/docs/          # Versioned tglow-core Markdown
│   ├── edit-quant/docs/          # Versioned edit-quant Markdown
│   └── proliferation-analysis/docs/ # Versioned ProliferationAnalysis Markdown
├── theme/                        # React layout and styles
├── scripts/                      # Content build helpers
├── rspress.config.ts             # Main portal configuration
└── .github/workflows/pages.yml   # Production and preview deployment

doc_build/, node_modules/, and theme/generated/ are generated locally and must not be committed.

Changes that require a maintainer

• Changing the homepage layout, banner, research placeholders, navigation, or theme.
• Adding a new software tool to the navigation and build workflow.
• Registering a new released documentation version.
• Adding a new page to a tool's ordered sidebar.
• Changing GitHub Pages or deployment behavior.

Add a released documentation version

1. Copy the prior version under software/<tool>/docs/<new-version>/.
2. Update the Markdown for that release.
3. Add the release to multiVersion.versions in software/software-config.ts.
4. Change currentVersion only when the release should become the default.

Local development

Install dependencies and run the portal development server:

npm install
npm run dev

Build and preview the portal and both software documentation sites together:

npm run build
npm run preview -- --host 0.0.0.0 --port 51303

Before merging, verify the main page, publications, both software roots, all changed version routes, navigation links, and narrow-screen text overflow.