GenSpectrum

We develop open web APIs and dashboards for genomic epidemiology. Monkeypox - and SARS-CoV-2 -

[GenSpectrum @GenSpectrum]

Thank you very much to the UShER team (Jakob McBroome, @AngieSHinrichs, @RussCorbett, @yatishturakhia, and many more) for providing the daily-updated trees, @theosanderson for developing Taxonium (and adding several features upon request!) and @CDC_AMD for funding. 4/4

[GenSpectrum @GenSpectrum]

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

[GenSpectrum @GenSpectrum]

The feature is only available on https://t.co/Bl8B4ScWuY which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.

If you have any questions or suggestions, please let us know! 3/4

[GenSpectrum @GenSpectrum]

We have just received an updated dataset from GISAID. Many thanks to the GISAID team for fixing the data feed!

[GenSpectrum @GenSpectrum]

Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.

[GenSpectrum @GenSpectrum]

Information for CoV-Spectrum users: The GISAID data on CoV-Spectrum has not been updated since 23 December due to an interruption in the data feed. We have contacted GISAID regarding this issue and are hopeful for a resolution soon.

[GenSpectrum @GenSpectrum]

GenSpectrum just added a mpox dashboard using data from @Pathoplexus – see https://t.co/YFxRxaOePa

[GenSpectrum @GenSpectrum]

We would like to thank all the data generators for making their data openly available, @ETH_en, the US @CDCgov and the Office of Advanced Molecular Detection (@CDC_AMD) for funding and the whole team (https://t.co/ateF5TfFyH) for the amazing work! 5/5

[GenSpectrum @GenSpectrum]

Our new https://t.co/niy9q7b3g3 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

[GenSpectrum @GenSpectrum]

Our tool is of course fully open source. Please let us know if you have any feedback or a suggestion for what should be added or improved. You can create an issue in our GitHub repository: https://t.co/YYUf6cL11e 4/5

[Tanja Stadler @TanjaStadler_CH]

It was an amazing journey for us (our research team @ETH_en with the support of contracted software developers from TNG technology) to work with colleagues across the globe from the first idea to what we now call Pathoplexus https://t.co/krMM3TN9hr! We are very proud to 1/2

[Pathoplexus @pathoplexus]

💡 Want to learn more or get involved? Visit https://t.co/4wGez2nTCr, follow us here, or join the discussion on our forums (https://t.co/BtmD6Fyas5)!

Together, we can create a more equitable & collaborative environment for global pathogen research! 🎉 #Pathoplexus

14/14

[Pathoplexus @pathoplexus]

📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬
Launching with 4 viruses, https://t.co/4wGez2nTCr combines modern open-source software with transparent governance to improve global pathogen sequence sharing.

1/14

[GenSpectrum @GenSpectrum]

Interested in developing dashboards and tools for public health and genomic epidemiology? We are looking for a software engineer to join our GenSpectrum team at @ETH_BSSE in Basel, 🇨🇭CH!

https://t.co/2uu0JTj1Fi

Please reach out if you have any questions and please share! :)

[GenSpectrum @GenSpectrum]

CoV-Spectrum now uses the most recent Nextclade dataset and calls BA.2.86. https://t.co/NBPLVFaS4y

[Tanja Stadler @TanjaStadler_CH]

You can now use a chatbot to find out latest information about SARS-CoV-2 variants https://t.co/zuAicfNbNC https://t.co/uTy46Lwsj7 @GenSpectrum in your favorite language, including Swiss German! The chat relies on the millions of available SARS-CoV-2 sequences, answering 1/2

[GenSpectrum @GenSpectrum]

@LittleFunnyGeek @TanjaStadler_CH @OpenAI Yes, exactly!

[GenSpectrum @GenSpectrum]

@LittleFunnyGeek @TanjaStadler_CH @OpenAI ...without seeing the previous question. This is the text that comes after the result table. That means that if the text fits to the question, the results should be correct. However, this is the first prototype and more evaluation is needed to be really sure.

[GenSpectrum @GenSpectrum]

@LittleFunnyGeek @TanjaStadler_CH @OpenAI ChatGPT is used to transform the question to a database query which is then executed by our internal database. As we don't directly take information from ChatGPT, the results should be quite reliable. To avoid/identify "misunderstanding", ChatGPT is asked to explain the query...