init concept for tutorials

Author: jjkoehorst

.github/workflows/deploy.yml

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+name: Deploy Jupyter Book to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Build the book
+        env:
+          BASE_URL: /tutorials
+        run: |
+          jupyter-book build --html --no-serve
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: '_build/html'
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

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+# Jupyter Book build output
+_build/
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+*.egg-info/
+.eggs/
+dist/
+build/
+
+# Jupyter Notebook
+.ipynb_checkpoints/
+*.ipynb_checkpoints
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Secrets
+.env
+*.env

README.md

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+# FAIRDOM-SEEK Tutorials
+
+Tutorials for working with FAIRDOM-SEEK, built with Jupyter Book v2.
+
+## View Online
+
+Visit the tutorials at: https://seek4science.github.io/tutorials/
+
+## Local Development
+
+### Prerequisites
+
+- Python 3.8+
+- Node.js 18+
+- pip
+
+### Setup
+
+```bash
+# Create a virtual environment (optional but recommended)
+python -m venv .venv
+source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+
+# Install dependencies
+pip install -r requirements.txt
+```
+
+### Build and preview locally
+
+```bash
+# Build and start dev server
+jupyter-book build --html
+
+# Or for local testing without base URL
+BASE_URL="" jupyter-book build --html
+```
+
+The dev server starts automatically at http://localhost:3000 (or next available port).
+
+### Adding new content
+
+1. Create a new `.md` or `.ipynb` file in the appropriate directory
+2. Add the file to `myst.yml` under the `toc` section
+3. Build and preview locally
+4. Commit and push to deploy
+
+## Deployment
+
+The book is automatically built and deployed to GitHub Pages when changes are pushed to the `main` branch.
+
+### GitHub Pages Setup
+
+1. Go to repository Settings > Pages
+2. Under "Build and deployment", select "GitHub Actions" as the source
+3. The workflow will automatically deploy on push to main

images/.gitkeep

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+# UNDER DEVELOPMENT
+
+This book is currently under development. Content may change frequently and is not yet complete. Please check back later for the finalized version.
+
+## Welcome to FAIRDOM-SEEK Tutorials
+
+This book contains tutorials and guides for working with FAIRDOM-SEEK.
+
+## What is FAIRDOM-SEEK?
+
+FAIRDOM-SEEK is a web-based platform for sharing heterogeneous scientific research datasets, models, simulations, processes, and research outcomes. It supports FAIR (Findable, Accessible, Interoperable, Reusable) data management principles.
+
+## Contents
+
+This book is organized into the following sections:
+
+- **[Introduction Tutorial](tutorials/introduction.md)** - Getting started with SEEK basics
+- **[Advanced Tutorial](tutorials/advanced.md)** - Power user features and administration
+- **[API Tutorial](tutorials/api.md)** - Programmatic access via the JSON API
+- **Notebooks** - Interactive Jupyter notebook examples
+
+## Resources
+
+- [FAIRDOM-SEEK Documentation](https://docs.seek4science.org)
+- [FAIRDOMHub](https://fairdomhub.org) - Public SEEK instance
+- [FAIRDOM Community](https://fair-dom.org)
+- [GitHub Repository](https://github.com/seek4science/seek)

images/favicon.png

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+version: 1
+project:
+  title: FAIRDOM-SEEK Tutorials
+  authors:
+    - name:
+        literal: FAIRDOM-SEEK
+  github: https://github.com/seek4science/tutorials
+  toc:
+    - file: intro.md
+    - title: Introduction Tutorials
+      file: tutorials/introduction/index.md
+      children:
+        - file: tutorials/introduction/overview.md
+        - file: tutorials/introduction/getting-started.md
+        - file: tutorials/introduction/isa-structure.md
+        - file: tutorials/introduction/uploading-data.md
+        - file: tutorials/introduction/sharing.md
+    - title: Advanced Tutorials
+      file: tutorials/advanced/index.md
+      children:
+      - file: tutorials/advanced.md
+      - file: tutorials/api.md
+      - file: notebooks/example.ipynb
+    - title: Workshops
+      file: workshops/index.md
+      children:
+        - file: workshops/workshop-bioind4-2026-02.md
+      
+
+site:
+  title: FAIRDOM-SEEK Tutorials
+  options:
+    favicon: "./images/favicon.png"
+    logo: "./images/favicon.png"
+    logo_text: FAIRDOM-SEEK Tutorials
+    base_url: /tutorials
+    hide_footer_links: true
+  actions:
+    - title: GitHub
+      url: https://github.com/seek4science/tutorials
+  template: book-theme

intro.md

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+@article{seek2015,
+  title={SEEK: a systems biology data and model management platform},
+  author={Wolstencroft, Katherine and others},
+  journal={BMC Systems Biology},
+  volume={9},
+  number={1},
+  pages={33},
+  year={2015},
+  publisher={BioMed Central}
+}

myst.yml

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+jupyter-book>=2.0.0