iiinova — where your digital self keeps evolving

Chaoran Chen

@chaoranchen.de

459 followers 108 following 23 posts

Scientific software engineer at ETH Zurich, founder of GenSpectrum.org, co-founder of Pathoplexus.org, always looking for recommendations for board games 🎲 and books 📚

Posts Replies Media

Chaoran Chen @chaoranchen.de · 28/08/2025

Finally, CoV-Spectrum is meeting trees 🌳 – this week, we released a new feature to browse the SARS-CoV-2 UShER tree on CoV-Spectrum. With the new feature, you can see a subtree of your variant of interest. 1/4

1228

Chaoran Chen @chaoranchen.de · 16/12/2024

GenSpectrum just added a mpox dashboard using data from @pathoplexus.org – see genspectrum.org

020

Chaoran Chen @chaoranchen.de · 30/11/2024

Thank you, Swiss Academies, for awarding @pathoplexus.org with the National ORD prize! To summarize our lightning talk and our fundamental beliefs: (1) It is crucial to make it easy to share and use data which includes having a user-friendly interface, a simple API and good documentation. 1/3

Our foundation for open data:
- Easy to share and use
- Allows time-limited protection
- Gives credit to data submitters
- Transparent and democratic governance

150

Chaoran Chen @chaoranchen.de · 25/11/2024

We also offer a Loculus instance with H5N1 and RSV data from INSDC, providing a new website and API to access the data. You can find both aligned and unaligned sequences and lineage annotations. For H5N1, the sequences from different segments have been linked together. loculus.genspectrum.org 3/5

131

Chaoran Chen @chaoranchen.de · 25/11/2024

In the "Analyze a single variant" view, you can query a variant by lineage and mutations and see its spatio-temporal distributions and mutations (over time). The "Sequencing efforts" view displays the number of sequences, their geographic origins and the contributors 2/5

131

Chaoran Chen @chaoranchen.de · 25/11/2024

Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5

46933