FAQ

Frequently asked questions about ProtSpace.

General

Do I need machine learning knowledge?

No. ProtSpace is designed for biologists and researchers - you only need protein embeddings.

Is my data uploaded to a server?

No. Everything runs in your browser - your data never leaves your computer.

Which file formats are supported?

Only .parquetbundle files. See Using Google Colab for how to generate them.

Can I use it offline?

Yes, after initial page load. Note: 3D structure loading requires internet.

Is it free?

Yes. ProtSpace is open source under the Apache 2.0 license.

Data

How do I generate a .parquetbundle?

• Google Colab notebook - No installation (recommended)
• Python CLI - For local processing or automation

What is the recommended dataset size?

Size	Performance
< 10K proteins	Optimal - smooth experience
10K - 500K	Good - may slow on older devices
> 500K	Challenging - consider subsetting

Browser performance varies by device and GPU capabilities.

Can I add custom annotations?

Yes. Add columns when generating the bundle. See Data Format.

How do I include 3D structures?

Structures load automatically from AlphaFold if your protein IDs are UniProt accessions.

Visualization

Can I customize colors?

Currently, colors are automatically generated. Custom color schemes will be supported in future versions.

What are multi-label annotations?

Annotations with multiple values per protein (e.g., multiple EC numbers). Displayed as pie charts.

Performance

The browser is slow or freezing

1. Use Chrome for best performance
2. Reduce dataset size

Which browser works best?

Browser	Performance
Chrome	Best
Brave	Best
Edge	Excellent
Safari	Good
Firefox	Slower

Can I visualize 1 million proteins?

Not recommended. Performance degrades above 500K proteins - consider subsetting.

Technical

What are the system requirements?

Browser: Modern browser with WebGL 2.0 support

• Chrome 80+
• Firefox 75+
• Safari 13.1+
• Edge 80+

Hardware: Any modern computer. Better GPU = better performance.

What's inside a .parquetbundle?

Three Parquet files bundled together:

1. Annotation data (protein metadata)
2. Projection metadata (methods, parameters)
3. Projection coordinates (x, y, z)

See Data Format for details.

Contributing

How can I contribute?

See CONTRIBUTING.md on GitHub.

Where do I report bugs?

GitHub Issues

Can I request features?

Yes! Open an issue or start a discussion on GitHub.

Citation

How do I cite ProtSpace?

Senoner, T., et al. (2025). ProtSpace: A Tool for Visualizing Protein Space.
Journal of Molecular Biology. DOI: 10.1016/j.jmb.2025.168940

BibTeX:

@article{senoner2025protspace,
  title={ProtSpace: A Tool for Visualizing Protein Space},
  author={Senoner, T. and others},
  journal={Journal of Molecular Biology},
  year={2025},
  doi={10.1016/j.jmb.2025.168940}
}

Still Have Questions?

• GitHub Discussions: Ask the community
• Issues: Report bugs