ISB Dataset Portal

A lightweight static HTML portal for browsing Integrated Structural Biology (ISB) multi-technique datasets from SciLifeLab facilities.

Overview

This portal provides an overview of datasets that combine multiple experimental and computational techniques, including:

• Cryo-EM
• X-ray crystallography
• SAXS/SANS
• NMR
• Mass spectrometry/Proteomics
• Biophysics
• Molecular dynamics simulations
• Integrative computational modeling

Each dataset has its own dedicated page with detailed information and links to public repositories (PDB, EMDB, EMPIAR, SASBDB, SciLifeLab Data Repository, etc.).

Visual Identity

This portal uses the official SciLifeLab visual identity:

• Colors: Lime (#A7C947), Teal (#045C64), Aqua (#4C979F), Grape (#491F53)
• Typography: Lato (headlines) and Lora (body text) from Google Fonts

Structure

isb_simple_portal/
├── index.html              # Main index page with all datasets
├── datasets/               # Individual dataset pages
│   ├── dataset-1.html     # GLIC lipid-binding & gating
│   ├── dataset-2.html     # DeCLIC Ca²⁺-stabilised N-terminal domain
│   ├── dataset-3.html     # MUC2 CysD2 domain
│   ├── dataset-4.html     # MecA/ClpC/ClpP AAA⁺ protease
│   ├── dataset-5.html     # FusB-mediated rescue of EF-G from fusidic acid
│   └── dataset-6.html     # Sodium caprate scattering + CG-MD
├── css/
│   └── style.css          # Stylesheet with SciLifeLab branding
└── README.md              # This file

GitHub Pages Setup

This portal is designed to be hosted on GitHub Pages. To set it up:

1. Push this repository to GitHub

   git init
   git add .
   git commit -m "Initial commit: ISB Dataset Portal"
   git branch -M main
   git remote add origin https://github.com/YOUR_USERNAME/YOUR_REPO_NAME.git
   git push -u origin main

2. Enable GitHub Pages

   • Go to your repository on GitHub
   • Navigate to Settings → Pages
   • Under Source, select Deploy from a branch
   • Choose main branch and / (root) folder
   • Click Save

3. Access your site

   • Your site will be available at: https://YOUR_USERNAME.github.io/YOUR_REPO_NAME/
   • It may take a few minutes for the site to be available after enabling Pages

Local Development

To view the portal locally:

1. Clone the repository:

   git clone https://github.com/YOUR_USERNAME/YOUR_REPO_NAME.git
   cd YOUR_REPO_NAME

2. Open index.html in a web browser, or use a local server:

   # Using Python 3
   python3 -m http.server 8000
   
   # Using Python 2
   python -m SimpleHTTPServer 8000
   
   # Using Node.js (if you have http-server installed)
   npx http-server

3. Navigate to http://localhost:8000 in your browser

Features

• Clean, responsive design using SciLifeLab visual identity
• Repository links automatically parsed and linked to:
  • PDB (RCSB)
  • EMDB (Electron Microscopy Data Bank)
  • EMPIAR (Electron Microscopy Public Image Archive)
  • SASBDB (Small Angle Scattering Biological Data Bank)
  • SciLifeLab Data Repository (via DOI)
  • Other repositories as available
• Technique badges showing which methods were used for each dataset
• Simple navigation between index and individual dataset pages

Data Source

The datasets are sourced from the ISB multi-technique inventory CSV file. Each dataset entry includes:

• Unit/Facility information
• System/target description
• Organism/source
• Techniques used
• Public repository links and IDs
• Data collection years
• Access/reuse status

Monitoring New Datasets

A monitoring system is available to track new multimodal dataset depositions from SciLifeLab's ISB platform.

Quick Start

Run the monitoring script manually:

python scripts/monitor_datasets.py

Automated Monitoring

A GitHub Actions workflow (.github/workflows/monitor.yml) runs weekly to check for new datasets. Results are saved as artifacts.

Manual Monitoring

Many repositories require manual checking due to API limitations. See scripts/MONITORING.md for:

• Weekly manual check checklist
• Monthly deep dive procedures
• Criteria for adding new datasets
• Step-by-step instructions for each repository

Adding New Datasets

When a new multimodal dataset is discovered:

1. Create datasets/dataset-N.md following the existing template
2. Update index.html to add the new dataset card
3. Run python scripts/build.py to generate HTML

Notes

• The .nojekyll file is included to prevent GitHub Pages from processing the site with Jekyll (not needed for static HTML)
• All paths are relative, making the site portable and GitHub Pages compatible
• The portal excludes "Internal notes" as they are marked as "not public"

License

This portal is part of SciLifeLab's ISB initiative. Please refer to SciLifeLab's policies for usage and attribution.

Contact

For questions or suggestions about this portal, please contact the SciLifeLab ISB team.