GenSpectrum

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GenSpectrum

GenSpectrum

@GenSpectrum

We develop open web APIs and dashboards for genomic epidemiology. Monkeypox - https://t.co/ehHkFkSaKl and SARS-CoV-2 - https://t.co/feDGaT1cNx

D-BSSE@ETH, Basel, Switzerland Katılım Ekim 2021
21 Takip Edilen1.4K Takipçiler
GenSpectrum
GenSpectrum@GenSpectrum·
The feature is only available on open.cov-spectrum.org 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
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GenSpectrum
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
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GenSpectrum
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.
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GenSpectrum
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 (#contributors-" target="_blank" rel="nofollow noopener">github.com/GenSpectrum#co…) for the amazing work! 5/5
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GenSpectrum
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: github.com/GenSpectrum/da… 4/5
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GenSpectrum
GenSpectrum@GenSpectrum·
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
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Tanja Stadler
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 pathoplexus.org! We are very proud to 1/2
Pathoplexus@pathoplexus

📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14

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Pathoplexus
Pathoplexus@pathoplexus·
💡 Want to learn more or get involved? Visit Pathoplexus.org, follow us here, or join the discussion on our forums (discussion.pathoplexus.org)! Together, we can create a more equitable & collaborative environment for global pathogen research! 🎉 #Pathoplexus 14/14
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Pathoplexus
Pathoplexus@pathoplexus·
📢 We're excited to introduce Pathoplexus, a specialized sequence database for human viral pathogens! 🌍 🧬 Launching with 4 viruses, Pathoplexus.org combines modern open-source software with transparent governance to improve global pathogen sequence sharing. 1/14
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GenSpectrum
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! jobs.ethz.ch/job/view/JOPG_… Please reach out if you have any questions and please share! :)
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Tanja Stadler
Tanja Stadler@TanjaStadler_CH·
You can now use a chatbot to find out latest information about SARS-CoV-2 variants arxiv.org/abs/2305.13821 cov-spectrum.org/chat @GenSpectrum in your favorite language, including Swiss German! The chat relies on the millions of available SARS-CoV-2 sequences, answering 1/2
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Tanja Stadler
Tanja Stadler@TanjaStadler_CH·
Do you want to find out details about the circulating SARS-CoV-2 variants? Then chat to cov-spectrum.org/chat - it can provide answers to questions for which even the cov-spectrum.org dashboard has no direct information. We would be grateful if you allow the 1/2
GenSpectrum@GenSpectrum

💬 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 cov-spectrum.org/chat. It can even answer questions that the dashboard can’t! 🚀 Here are some examples. 1/

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GenSpectrum
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.
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GenSpectrum
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...
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Keşfet

@AngieSHinrichs @RussCorbett @yatishturakhia @theosanderson @CDC_AMD @Pathoplexus @ETH_en @CDCgov