We develop open web APIs and dashboards for genomic epidemiology. Monkeypox - https://xitter.cf/t.co/ehHkFkSaKl and SARS-CoV-2 - https://xitter.cf/t.co/feDGaT1cNx
D-BSSE@ETH, Basel, Switzerland
Joined October 2021
- Tweets169
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GenSpectrum retweeted
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
📢 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
GenSpectrum retweeted
💡 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
GenSpectrum retweeted
📢 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
GenSpectrum retweeted
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
GenSpectrum retweeted
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
💬 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/
GenSpectrum retweeted
Here it is variant chatbot! This is likely among the best possible uses for AI to manage big data at the time of a pandemic ! @EricTopol @DrEricDing @TRyanGregory @RobiVil @PeacockFlu
💬 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/
GenSpectrum retweeted
Incredibly honored to be featured in the Nature piece below by @maxdkozlov. I never expected anything resembling this kind of recognition, & it all still feels a bit surreal. I want to mention a few of the people whose work & generosity has been vitally important to me. 1/
Hoping to help with the pandemic in any way they can, a motley crew of self-taught citizen scientists scour millions of SARS-CoV-2 genomes for problematic mutations — all for no pay.
Meet Ryan Hisner (@LongDesertTrain), a rural school teacher from Indiana
nature.com/articles/d41586-0…
GenSpectrum retweeted
One of the most important reasons why we shouldn't gatekeep access to science or data - anyone can do amazing things, create amazing resources, & contribute amazing insights - & we all benefit!
We never know what we don't know due to someone not being 'allowed' to try!
Good article by @maxdkozlov about the unusual path that @LongDesertTrain has taken to become one of the leading experts on #SARSCoV2 variants.
nature.com/articles/d41586-0…
GenSpectrum retweeted
As usual @GenSpectrum helps us dig into this at CoVSpectrum:
cov-spectrum.org/explore/Wor…
Looking at "Mutations over time", we can see really nicely that BM.1.1.1* was mostly S:486S earlier, then 486P later - likely a daughter lineage outgrowing 'original' BM.1.1.1!
2/5
GenSpectrum retweeted
We are happy to announce a dashboard providing the effective reproductive number for influenza based on wastewater wise.ethz.ch/influenza/. We update the dashboard as data comes in. The estimates are compared to estimates based on case data, showing generally a good 1/2
GenSpectrum retweeted
The decreasing SARS-COV-2 🧬 data could impact our ability to track its evolutionary trends. However, it's important to remember that 🧬 are the data, But it's analysis platforms like @nextstrain , USHER, and @GenSpectrum that enable the extraction of knowledge out of it.
1/4
GenSpectrum retweeted
#Mastodon users can now follow mstdn.science/web/@chaoranch… for news about GenSpectrum.
I'll also give #Mastodon a try. From now on, I will also post @GenSpectrum / CoV-Spectrum news from mstdn.science/web/@chaoranch….
Thanks, @happy_khan, for setting up the mstdn.science server!
GenSpectrum retweeted
The asterisk comes from @GenSpectrum, it means "and descending lineages." The reason is many tools treat the label BA.5.2 as "BA.5.2, except for whatever sublineages have been carved out of it as of the time of the toolset version," so you search BA.5.2* to include sublineages
GenSpectrum retweeted
🔔 REAL TIME COVID19 MONOCLONAL ANTIBODY BY COUNTRY 🔔.
I want to share with you the online freely accessible collection that I have just created here: cov-spectrum.org/collections…. 🧵@EricTopol @kakape @ewencallaway @mildanalyst @TRyanGregory @DrEricDing #IDTwitter
GenSpectrum retweeted
Thank you very much, @K_G_Andersen! I'm looking forward to the next innovations on outbreak.info😉
And thanks to all the amazing users who submitted hundreds of suggestions on Github and maintain the collections. We're grateful for your support!
GenSpectrum retweeted
Here's the full, frequently updated list cov-spectrum.org/collections… @GenSpectrum
Thanks to so many keeping a close eye on these, including @siamosolocani @CorneliusRoemer @PeacockFlu @SolidEvidence @LongDesertTrain @richardneher and others 🙏
GenSpectrum retweeted
Submitting to @NCBI can be intimidating -- but no more! Getting your #monkeypox sequences up is as simple as following this guide!
Thanks to NCBI & of course to all scientists worldwide contributing to #opendata #openscience
To all monkeypox sequencers:
@NCBI has written a nice step-by-step guide on how to submit monkeypox sequences to Genbank via their Bankit tool:
ncbi.nlm.nih.gov/genbank/mon…
GISAID will automatically copy the sequences - thus no need to submit twice if you want to save time.
GenSpectrum retweeted
You can also look up #monkeypox lineages - as well as browse & download sequences by time, geographic distribution & mutations - on MpoxSpectrum @GenSpectrum via website or API.
Website: mpox.genspectrum.org
API docs: lapis-docs.readthedocs.io/en…
8/12
GenSpectrum retweeted
An international cohort of scientists, many of whom helped propose the new #monkeypox clade names in June, have formed a group to designate new monkeypox lineages.
Initially, 5 new lineages stemming from the B.1 ('outbreak') clade have been designated.
1/12
GenSpectrum retweeted
It’s now easier than ever to submit data to the #COVID19 Data Portal. Our handy data submission decision tree helps you find the correct repository in three easy steps.
covid19dataportal.org/news/c…