Chaoran Chen
@chaoranchen.de
Scientific software engineer at ETH Zurich, founder of GenSpectrum.org, co-founder of Pathoplexus.org, always looking for recommendations for board games 🎲 and books 📚
Pinned
Chaoran Chen
@chaoranchen.de
· Nov 25
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.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
Reposted by Chaoran Chen
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 6, 2025 at 9:46 PM
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Reposted by Chaoran Chen
Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝
A fantastic turnout & wonderful time spent with curious users!
A fantastic turnout & wonderful time spent with curious users!
October 27, 2025 at 7:58 AM
Thrilled & honoured to have run the first @pathoplexus.org workshop with @chaoranchen.de @pagasi.bsky.social @kanyerezi30.bsky.social & Arthur Shem Kasambula at @pha4ge.bsky.social on Saturday! 🎉🤝
A fantastic turnout & wonderful time spent with curious users!
A fantastic turnout & wonderful time spent with curious users!
Reposted by Chaoran Chen
PI's of BSky: If you had to guess, What percentage of 2nd+ year PhD students in your lab have an @orcid.org?
October 16, 2025 at 5:02 PM
PI's of BSky: If you had to guess, What percentage of 2nd+ year PhD students in your lab have an @orcid.org?
Reposted by Chaoran Chen
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
October 16, 2025 at 7:48 PM
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
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
August 28, 2025 at 7:41 AM
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
Reposted by Chaoran Chen
🗓 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
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
August 27, 2025 at 3:57 PM
🗓 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
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
If you would like to find out more about Loculus, you can still register for the Loculus tutorial at the [BC]2 Basel Computational Biology Conference 2025 on 8 September! Registration closes on 1 September.
www.bc2.ch/tutorials-wo...
www.bc2.ch/tutorials-wo...
“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
August 11, 2025 at 10:07 AM
If you would like to find out more about Loculus, you can still register for the Loculus tutorial at the [BC]2 Basel Computational Biology Conference 2025 on 8 September! Registration closes on 1 September.
www.bc2.ch/tutorials-wo...
www.bc2.ch/tutorials-wo...
Reposted by Chaoran Chen
“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
August 11, 2025 at 8:09 AM
“Loculus is remarkable for enabling efficient and secure sharing of pathogen genomic data, which is crucial for public health responses to infectious diseases."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
Reposted by Chaoran Chen
Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️
Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss) in Basel, run by @chaoranchen.de & Anya Parker! 🧬
Register: www.bc2.ch/registration...
#bioinformatics #openScience
Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss) in Basel, run by @chaoranchen.de & Anya Parker! 🧬
Register: www.bc2.ch/registration...
#bioinformatics #openScience
August 8, 2025 at 8:46 AM
Interested to learn about how to run your own Loculus (the database code behind @pathoplexus.org)? 🤔🖥️
Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss) in Basel, run by @chaoranchen.de & Anya Parker! 🧬
Register: www.bc2.ch/registration...
#bioinformatics #openScience
Sign up for the Loculus Tutorial on Mon 8 Sept at BC2 Conference (@sib.swiss) in Basel, run by @chaoranchen.de & Anya Parker! 🧬
Register: www.bc2.ch/registration...
#bioinformatics #openScience
Reposted by Chaoran Chen
Loculus, an open-source software for building pathogen sequencing databases, is on the shortlist for #SIBRemarkableOutputs 2024. It’s a joint project by the teams of @neher.io, @tanjastadler.bsky.social and @firefoxx66.bsky.social xx66.bsky.social. Congratulations!
💡 The SIB Remarkable Outputs 2024 are out !
This shortlist of the most outstanding works produced by SIB members in 2024 showcase the latest advances in the Swiss bioinformatics field. Attend their presentations at [BC]2!
👉 Discover this shortlist of outstanding works
www.sib.swiss/remarkable-o...
This shortlist of the most outstanding works produced by SIB members in 2024 showcase the latest advances in the Swiss bioinformatics field. Attend their presentations at [BC]2!
👉 Discover this shortlist of outstanding works
www.sib.swiss/remarkable-o...
August 4, 2025 at 2:00 PM
Loculus, an open-source software for building pathogen sequencing databases, is on the shortlist for #SIBRemarkableOutputs 2024. It’s a joint project by the teams of @neher.io, @tanjastadler.bsky.social and @firefoxx66.bsky.social xx66.bsky.social. Congratulations!
Reposted by Chaoran Chen
📢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
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
July 25, 2025 at 10:44 AM
📢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
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
Reposted by Chaoran Chen
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility!
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
July 15, 2025 at 10:13 AM
🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility!
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update
1/9
Reposted by Chaoran Chen
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
May 28, 2025 at 11:02 PM
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Reposted by Chaoran Chen
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
May 22, 2025 at 4:06 PM
📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.
1/4
Reposted by Chaoran Chen
🤔Interested in building and managing microbial genomic databases? Join the hands-on tutorial on #Loculus & learn how to set up, customize & deploy Loculus for your projects.
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb
May 13, 2025 at 1:29 PM
🤔Interested in building and managing microbial genomic databases? Join the hands-on tutorial on #Loculus & learn how to set up, customize & deploy Loculus for your projects.
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb
🔹 Tutorial organized by @chaoranchen.de & Anna Parker, from @ethz.ch
📆8 sept at #BC2Basel
👉 Register: tinyurl.com/5n8w3pwb
Reposted by Chaoran Chen
🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
Home
Using the MLST hash template as an example genomic epi database
lskatz.github.io
April 28, 2025 at 12:41 PM
🚀 New proof-of-principle:
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
An interactive, searchable MLST hash database... all in your browser! 🔥
Live demo ➡️ lskatz.github.io/mlst-hash-te...
A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te...
🧵
Reposted by Chaoran Chen
Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
Application deadline extended for Taming the BEAST in Beijing!
taming-the-beast.org
April 17, 2025 at 7:28 PM
Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
The time is flying by.. Hard to believe that it has already been 7 months since we started Pathoplexus!
🗓️ Pathoplexus has now been around for 7 months!
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
Pathoplexus | Pathoplexus Spring 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
April 16, 2025 at 3:51 PM
The time is flying by.. Hard to believe that it has already been 7 months since we started Pathoplexus!
Reposted by Chaoran Chen
🗓️ Pathoplexus has now been around for 7 months!
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
Pathoplexus | Pathoplexus Spring 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
April 16, 2025 at 3:47 PM
🗓️ Pathoplexus has now been around for 7 months!
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
And both we and our users have been busy - so we wanted to share some updates & highlights!
📰 You can see our full News Item here: pathoplexus.org/news/2025-04-16-spring-update
1/9
Reposted by Chaoran Chen
I think I may buy a few dozen copies of this book and just hand them out to strangers.
bookshop.org/p/books/who-...
bookshop.org/p/books/who-...
Who Is Government?: The Untold Story of Public Service
The Untold Story of Public Service
bookshop.org
April 6, 2025 at 3:30 PM
I think I may buy a few dozen copies of this book and just hand them out to strangers.
bookshop.org/p/books/who-...
bookshop.org/p/books/who-...
Reposted by Chaoran Chen
The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss
SIB Swiss Institute of Bioinformatics | Data scientists for life
As a leading organization in biological and biomedical data science, SIB maximizes scientific impact through FAIR data, biodata resources, and innovation.
sib.swiss
February 4, 2025 at 7:33 AM
The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss
Reposted by Chaoran Chen
Today I have resigned from my position as a Data Editor at Proceedings B. I believe the journal does great work, but it feels wrong to voluntarily spend my time holding authors to account on behalf of the Royal Society, while the Society refuses to hold its own Fellows to account.
March 7, 2025 at 12:27 PM
Today I have resigned from my position as a Data Editor at Proceedings B. I believe the journal does great work, but it feels wrong to voluntarily spend my time holding authors to account on behalf of the Royal Society, while the Society refuses to hold its own Fellows to account.
Reposted by Chaoran Chen
Major cuts planned in SRF science journalism in Switzerland - the public service media. Scientists today launched a petition ‘Facts Instead of Misinformation: For Strong Science Journalism!’ Become one of over 1,800 signatories www.openpetition.eu/ch/petition/...
Facts Instead of Misinformation: For Strong Science Journalism! - Online-Petition
Open Letter from the Scientific Community to SRF Dear Management of SRG, Dear Executive Board of SRF, Dear Media and Science Policy Makers, We are deeply concerned about SRF’s plans to make significan...
www.openpetition.eu
February 10, 2025 at 8:36 PM
Major cuts planned in SRF science journalism in Switzerland - the public service media. Scientists today launched a petition ‘Facts Instead of Misinformation: For Strong Science Journalism!’ Become one of over 1,800 signatories www.openpetition.eu/ch/petition/...
Reposted by Chaoran Chen
Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...
February 5, 2025 at 2:52 PM
Thanks to huge efforts by Uganda’s Central Public Health Laboratory, Uganda Ministry of Health, UVRI, Africa CDC, & SANBI, UWC the sequence from the Ebola Sudan case in Kampala is now available on Pathoplexus pathoplexus.org/seq/PP_0011C... w full analysis here: virological.org/t/near-real-...