#Pathoplexus
LightNews LightNews
colincarlson.bsky.social
neither of these are intended to be data sharing platforms though, right? just workbenches? so insdc, cnsa, gisaid, pathoplexus all still upstream of them?
October 13, 2025 at 9:11 PM
pha4ge.bsky.social
Utilisation of Specialised Virus Genomic Databases Workshop

Learn to use Pathoplexus for data submission, metadata, & troubleshooting. With Emma Hodcroft, Chaoran Chen, Arthur Kasambula & Stephen Kanyerezi

Register: buff.ly/uTmq0db

#PHA4GECon2025
September 26, 2025 at 8:58 AM
theo.io
it was lots of fun to have the chance to chat pathoplexus with the microbinfie podcast team!
lskatz.github.io Lee Katz @lskatz.github.io · Sep 11
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
144 - micro binfie Pathoplexus part 1
pca.st
September 11, 2025 at 7:55 PM
happykhan.mstdn.science.ap.brid.gy
Just dropped: #microbinfie Pathoplexus Part 1!

Join Lee & guest Clint (and me) as we deep-dive with Emma Hodcroft, Theo Sanderson & Arthur Shem Kasambula about Pathoplexus […]
Original post on mstdn.science
mstdn.science
September 11, 2025 at 12:59 PM
lskatz.github.io
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
144 - micro binfie Pathoplexus part 1
pca.st
September 11, 2025 at 12:05 PM
pathoplexus.org
Since these sequences are likely to attract interest, it’s worth highlighting again what ‘Restricted-Use’ means on Pathoplexus.

Data Use Terms for Restricted-Use data: pathoplexus.org/about/terms-...

4/7
Screenshot of the Pathoplexus Data Use Terms, focusing on 4.2, Restricted Use Data introduction
September 10, 2025 at 10:00 AM
pathoplexus.org
We’re grateful these sequences were shared on Pathoplexus. The authors have chosen to share them as ‘Restricted-Use’ - enabling rapid access for public health, while limiting use in publications/preprints.

View the sequences here: pathoplexus.org/ebola-zaire/...

3/7
Screenshot of the search page on Pathoplexus showing the first 4 sequences: their Pathoplexus accession, sample date, collection country and subdivision, authors, affiliations, and length.
September 10, 2025 at 10:00 AM
firefoxx66.bsky.social
The EVE lab work & collaborations includes:
🌏 Tracking virus spread globally
🧬 Understanding virus evolution & immunity
📊 Building open tools like @Pathoplexus for transparent data sharing
🤝 Collaborating worldwide to better tackle pathogenic viruses

3/4
August 29, 2025 at 9:33 AM
firefoxx66.bsky.social
🔍 On our new site you can:

- Meet the EVE team 👥
- Explore our research on viral evolution & spread 🧬
- Explore our phylogenetic @nextstrain.org builds 🌳
- See the tools we build for analysis 🛠️
- Read about our publications & news 📰

2/4
Screenshot of the Collaborations page of the Eve-lab website, showing some of our collaborations: ARTIC2, Center for Pathogen Bioinformatics, ENPEN, ESCAPE, Pathoplexus, & VIM
August 29, 2025 at 9:33 AM
pathoplexus.org
📢 We’re also celebrating a successful ETH4D Research Challenge grant with ETH Zurich @ethz.ch & Stephen Kanyerezi (Uganda) @kanyerezi30.bsky.social to grow Pathoplexus & Loculus – with workshops, training, user feedback & community building.

9/10
An abstract image showing a world map made of small, colorful lines, as featured on ETH4D website, overlayed with the ETH4D logo itself.
August 27, 2025 at 3:57 PM
pathoplexus.org
🎉 New in August: Measles virus joins Pathoplexus!

Following strong community support, we added MeV data submission (with Open & Restricted-Use options, as always) and powerful search & data access for MeV
pathoplexus.org/measles/search

5/10
A screenshot of the Pathoplexus homepage, now showing Measles among the other pathogens supported.
August 27, 2025 at 3:57 PM
pathoplexus.org
And… 🏆
We received the 2024 Swiss National Open Research Data Prize for our commitment to openness & community governance – all while being powered largely by volunteer effort!

4/10
A photo of key members of the Pathoplexus developer team receiving the ORD prize
August 27, 2025 at 3:57 PM
pathoplexus.org
🗓 Pathoplexus turns ONE! 🎂🎉

In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...

1/10
An image of a birthday cake with scientific doodles around it, 9 colourful candles, and the Pathoplexus logo in the middle, with the words 'Happy 1 year'
August 27, 2025 at 3:57 PM
firefoxx66.bsky.social
Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!
lskatz.github.io Lee Katz @lskatz.github.io · Aug 25
@happykhan.mstdn.science.ap.brid.gy and I had a great time recording last week with @firefoxx66.bsky.social @theo.io and Arthur Shem, with the help of Clint. Episodes set to be released starting September 11.

#microbinfie
August 26, 2025 at 8:37 AM
Fantastic opportunity in Switzerland for a post-doc or dev, working on open-source tools to support global pathogen sequencing efforts (ARTIC2) and data sharing with protections for contributor's first-publication rights (Pathoplexus). 🧵
firefoxx66.bsky.social Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

1/5
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
July 25, 2025 at 11:39 PM
firefoxx66.bsky.social
What kinds of things will you be working on? ⚙️
- Design & deploy local genomic data storage solutions with Loculus 🧬
- Link ARTIC2 sequencing pipelines to Loculus & 1-click upload to Pathoplexus 🔗
- Integrate pathogen analytic pipelines into ARTIC2 software 🖥️

4/5
July 25, 2025 at 10:44 AM
firefoxx66.bsky.social
This is a unique opportunity to work on
- ARTIC2 (enabling affordable, portable, real-time sequencing)
- @pathoplexus.org (open-source platform redefining genetic sequence sharing)
- Loculus (Pathoplexus backend)

And make a tangible impact on global health & data equity! 🌍👐

2/5
July 25, 2025 at 10:44 AM
firefoxx66.bsky.social
📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

1/5
An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"
July 25, 2025 at 10:44 AM
ryanhisner.bsky.social
Amid the incessant barrage of depressing science news, the development of Pathoplexus is a refreshing contrast—thanks to the work of @theo.io, @arambaut.bsky.social, @firefoxx66.bsky.social, & others.

With funding, Pathoplexus could abolish the many insanities now plaguing genetic surveillance.
arambaut.bsky.social Andrew Rambaut @arambaut.bsky.social · Jul 15
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
Pathoplexus | Pathoplexus July Update
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
July 15, 2025 at 2:21 PM
arambaut.bsky.social
And of course a great way of supporting it is to submit your sequences there - and the best thing is it has an easy, low-friction, interface for submitting that means you avoid having to directly deal with genbank submission - Pathoplexus does it all for you.
July 15, 2025 at 2:05 PM
arambaut.bsky.social
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
Pathoplexus | Pathoplexus July Update
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
July 15, 2025 at 2:05 PM
pathoplexus.org
As you may have already seen, ARTIC2, follow-up to the hugely successful ARTIC, has launched, and through @firefoxx66.bsky.social & @swisstph.ch, Loculus (the software underlying Pathoplexus) is part of the effort to make sequencing & data sharing easier!

bsky.app/profile/path...

8/9
July 15, 2025 at 10:13 AM
pathoplexus.org
We’ve also made donating to Pathoplexus easier - our new Funding page has helpful information - we will add additional donation methods soon! And we’d be happy to discuss institutional support as well - just reach out! 💶
pathoplexus.org/about/funding

7/9
Pathoplexus | Funding
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
July 15, 2025 at 10:13 AM
pathoplexus.org
In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade!

Have a tool that would be worth including? See our docs!
pathoplexus.org/docs/how-to/...

5/9
July 15, 2025 at 10:13 AM
pathoplexus.org
Direct uploads in May & June have included the following sequences:
- 128 Mpox
- 15 West Nile
- 1089 RSV-A
- 1060 RSV-B
- 1 Ebola Zaire
An incredible diversity both in sequences and in contributing labs. We thank these contributors for choosing to share with Pathoplexus! 🙏🏻

3/9
July 15, 2025 at 10:13 AM