Chaoran Chen

134 Followers
47 Following
52 Posts
PhD student at ETH Zurich and developer of GenSpectrum (https://genspectrum.org, https://cov-spectrum.org)
GitHubhttps://github.com/chaoran-chen
GenSpectrum just added a mpox dashboard using data from @pathoplexus – see https://genspectrum.org
GenSpectrum Dashboards

GenSpectrum is an interactive dashboard to query and analyze pathogen sequences, currently available for Influenza H5N1, RSV, SARS-CoV-2 and the West Nile virus.

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. https://loculus.genspectrum.org 3/5
GenSpectrum | Home

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
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, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
Now, it’s your turn: please try it out and share your feedback with us! We would be grateful if you allow the conversations to be recorded: only if we know which questions you are interested in and how you phrase the questions, we can improve. You can rate the answers. 7/
What about non-human samples? Which are the other hosts? Note: When we first asked about minks, it looked for Mustela vision and couldn’t find anything. If we, however, specify the alternative name, Neovison vison, we get the right results. 5/
Many people wished to be able to search for a continent without a country (e.g. FedeGueli and @corneliusroemer). That is unfortunately not yet possible in the dashboard – but no problem for the chat! 4/
Let’s find out more about XBB.1.16. Which mutations does it have, when and where was it first observed, how many sequences were uploaded over time? 3/
First, let’s get an overview of the current situation: which lineages are circulating, which countries are sequencing, how did the sequencing effort change over time? 2/

💬 You can now chat with CoV-Spectrum! 💬

Backed by #OpenAI #ChatGPT (GPT-3.5), it’s now possible to ask questions about variants in a chat style at https://cov-spectrum.org/chat. It can even answer questions that the dashboard can’t! 🚀 Here are some examples. 1/

covSPECTRUM

covSPECTRUM is an interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2.