Enhancing multi-omic analyses through a federated microbiome analysis service https://osf.io/preprints/biohackrxiv/3x274 #Nextflow 🧬🖥️🧪
January 10, 2025 at 7:30 PM
Enhancing multi-omic analyses through a federated microbiome analysis service https://osf.io/preprints/biohackrxiv/3x274 #Nextflow 🧬🖥️🧪
"BioHackrXiv: Creating a federated publishing platform" https://doi.org/10.37044/osf.io/jh3m7_v1
"Overall goals are to have improved metadata and allow independence from OSF - though we
can operate in parallel. Ideally BioHackrXiv would be a template for a federated solution for
scientific […]
"Overall goals are to have improved metadata and allow independence from OSF - though we
can operate in parallel. Ideally BioHackrXiv would be a template for a federated solution for
scientific […]
Original post on fediscience.org
fediscience.org
September 22, 2026 at 10:03 AM
"BioHackrXiv: Creating a federated publishing platform" https://doi.org/10.37044/osf.io/jh3m7_v1
"Overall goals are to have improved metadata and allow independence from OSF - though we
can operate in parallel. Ideally BioHackrXiv would be a template for a federated solution for
scientific […]
"Overall goals are to have improved metadata and allow independence from OSF - though we
can operate in parallel. Ideally BioHackrXiv would be a template for a federated solution for
scientific […]
Keeping your research software metadata in sync across repositories and registries just got easier.
We’ve developed a bidirectional bridge between GitHub and bio.tools, helping you keep metadata up to date automatically.
Check out our BioHackrXiv preprint: doi.org/10.37044/osf...
We’ve developed a bidirectional bridge between GitHub and bio.tools, helping you keep metadata up to date automatically.
Check out our BioHackrXiv preprint: doi.org/10.37044/osf...
OSF
doi.org
February 26, 2026 at 7:09 AM
Keeping your research software metadata in sync across repositories and registries just got easier.
We’ve developed a bidirectional bridge between GitHub and bio.tools, helping you keep metadata up to date automatically.
Check out our BioHackrXiv preprint: doi.org/10.37044/osf...
We’ve developed a bidirectional bridge between GitHub and bio.tools, helping you keep metadata up to date automatically.
Check out our BioHackrXiv preprint: doi.org/10.37044/osf...
it is really sad that the Journal of Cheminformatics did not continue the Citation Typing Ontology Pilot. It has so much potential.
When I see how many people are adopting it in @biohackrxiv, I think it is a missed opportunity
When I see how many people are adopting it in @biohackrxiv, I think it is a missed opportunity
September 19, 2026 at 10:05 AM
it is really sad that the Journal of Cheminformatics did not continue the Citation Typing Ontology Pilot. It has so much potential.
When I see how many people are adopting it in @biohackrxiv, I think it is a missed opportunity
When I see how many people are adopting it in @biohackrxiv, I think it is a missed opportunity
BioHackrXiv authors can use Citation Typing Ontology (CiTO) citation intent annotations to express why they are citing the articles they cite. And many have! See https://doi.org/10.37044/OSF.IO/6RJVC and https://doi.org/10.5281/ZENODO.10072013
With 2026 […]
[Original post on fediscience.org]
With 2026 […]
[Original post on fediscience.org]
June 27, 2026 at 11:01 AM
BioHackrXiv authors can use Citation Typing Ontology (CiTO) citation intent annotations to express why they are citing the articles they cite. And many have! See https://doi.org/10.37044/OSF.IO/6RJVC and https://doi.org/10.5281/ZENODO.10072013
With 2026 […]
[Original post on fediscience.org]
With 2026 […]
[Original post on fediscience.org]
I wanted to be able to see all the BioHackathon with preprint reports in BioHackrXiv and RSS feeds for each meeting, to see all the cool hacking in biology
So, I hacked something up and now I can: https://egonw.github.io/bh-demo/
So, I hacked something up and now I can: https://egonw.github.io/bh-demo/
BioHackrXiv Preprints
Preprints for BioHackathons
egonw.github.io
May 29, 2025 at 12:10 PM
I wanted to be able to see all the BioHackathon with preprint reports in BioHackrXiv and RSS feeds for each meeting, to see all the cool hacking in biology
So, I hacked something up and now I can: https://egonw.github.io/bh-demo/
So, I hacked something up and now I can: https://egonw.github.io/bh-demo/
A new BioHackrXiv preprint describes public outputs from an international hybrid collaborative hackathon held at @cmu.edu, focusing on using machine learning methods to study the background genomic and environmental effects underlying complex genotype-phenotype relationships. bit.ly/bioinfohacka...
June 9, 2025 at 2:49 PM
A new BioHackrXiv preprint describes public outputs from an international hybrid collaborative hackathon held at @cmu.edu, focusing on using machine learning methods to study the background genomic and environmental effects underlying complex genotype-phenotype relationships. bit.ly/bioinfohacka...
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account
#introduction
#introduction
November 3, 2025 at 4:56 PM
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account
#introduction
#introduction
Did you know literature databases index preprints?
In Europe PMC you can discover preprints from 34 different preprint servers alongside peer reviewed research!
Since 2018, Europe PMC has made 1 million preprints searchable.
#OpenAccess #OpenScience #Preprint
In Europe PMC you can discover preprints from 34 different preprint servers alongside peer reviewed research!
Since 2018, Europe PMC has made 1 million preprints searchable.
#OpenAccess #OpenScience #Preprint
October 24, 2025 at 12:25 PM
Did you know literature databases index preprints?
In Europe PMC you can discover preprints from 34 different preprint servers alongside peer reviewed research!
Since 2018, Europe PMC has made 1 million preprints searchable.
#OpenAccess #OpenScience #Preprint
In Europe PMC you can discover preprints from 34 different preprint servers alongside peer reviewed research!
Since 2018, Europe PMC has made 1 million preprints searchable.
#OpenAccess #OpenScience #Preprint
🔍 #EPMCTopTips Tuesdays!
Tired of hopping between #preprint servers?
Search over 30 preprint servers all in one place with #EuropePMC!
We’ve got preprints from bioRxiv, medRxiv, Research square and more searchable in one go!
Check out the full list 👉 europepmc.org/Preprints#pr...
#PhDSky #MedSky
Tired of hopping between #preprint servers?
Search over 30 preprint servers all in one place with #EuropePMC!
We’ve got preprints from bioRxiv, medRxiv, Research square and more searchable in one go!
Check out the full list 👉 europepmc.org/Preprints#pr...
#PhDSky #MedSky
April 29, 2025 at 8:10 AM
🔍 #EPMCTopTips Tuesdays!
Tired of hopping between #preprint servers?
Search over 30 preprint servers all in one place with #EuropePMC!
We’ve got preprints from bioRxiv, medRxiv, Research square and more searchable in one go!
Check out the full list 👉 europepmc.org/Preprints#pr...
#PhDSky #MedSky
Tired of hopping between #preprint servers?
Search over 30 preprint servers all in one place with #EuropePMC!
We’ve got preprints from bioRxiv, medRxiv, Research square and more searchable in one go!
Check out the full list 👉 europepmc.org/Preprints#pr...
#PhDSky #MedSky
@biohackrxiv sounds great, will read soon! building a more sustainable foundation than pandoc would be a key step towards this. My experience contributing to pandoc/inara/the JOSS platform left a lot to be desired
September 22, 2026 at 10:10 AM
@biohackrxiv sounds great, will read soon! building a more sustainable foundation than pandoc would be a key step towards this. My experience contributing to pandoc/inara/the JOSS platform left a lot to be desired
I didn't know @biohackrxiv@fediscience.org preprint server was a thing - operated by OSF for preprinting works submitted in BioHackathons.
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
OSF
biohackrxiv.org
November 26, 2025 at 6:03 PM
I didn't know @biohackrxiv@fediscience.org preprint server was a thing - operated by OSF for preprinting works submitted in BioHackathons.
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
Always happy to check out new #preprint servers - I feel like that's where the most exciting ideas are found these days.
#bioinformatics
biohackrxiv.org
@cthoyt @biohackrxiv what would you replace @pandoc with? That part is actually the thing I am most confident with. We have ORCID, ROR, CiTO, CReDIT support, all with Pandoc.
But we would like to get people to submit a git (-hub) repository, and it would go from there.
But we would like to get people to submit a git (-hub) repository, and it would go from there.
September 22, 2026 at 10:17 AM
@cthoyt @biohackrxiv what would you replace @pandoc with? That part is actually the thing I am most confident with. We have ORCID, ROR, CiTO, CReDIT support, all with Pandoc.
But we would like to get people to submit a git (-hub) repository, and it would go from there.
But we would like to get people to submit a git (-hub) repository, and it would go from there.
@briannosek.bsky.social thanks, it looks good. I just had my first steps around, moderating BioHackrXiv prreprints and that moderation was quite intuitive!
I do run into a glitch: the page to search all BioHackrXiv preprints has unrelated content: https://osf.io/preprints/biohackrxiv/discover
I do run into a glitch: the page to search all BioHackrXiv preprints has unrelated content: https://osf.io/preprints/biohackrxiv/discover
October 12, 2025 at 5:31 AM
@briannosek.bsky.social thanks, it looks good. I just had my first steps around, moderating BioHackrXiv prreprints and that moderation was quite intuitive!
I do run into a glitch: the page to search all BioHackrXiv preprints has unrelated content: https://osf.io/preprints/biohackrxiv/discover
I do run into a glitch: the page to search all BioHackrXiv preprints has unrelated content: https://osf.io/preprints/biohackrxiv/discover
good luck to the participants of the SWAT4HCLS Biohackathon 2026 in the coming week! https://index.biohackrxiv.org/tag/SWAT4HCLS26
Use the hashtag to post your progress and have it show up on the BioHackRxiv #fediwall: https://guide.biohackrxiv.org/fediwall/
#swat4hcls26
Use the hashtag to post your progress and have it show up on the BioHackRxiv #fediwall: https://guide.biohackrxiv.org/fediwall/
#swat4hcls26
SWAT4HCLS Biohackathon 2026
Preprints for BioHackathons
index.biohackrxiv.org
March 21, 2026 at 4:59 PM
good luck to the participants of the SWAT4HCLS Biohackathon 2026 in the coming week! https://index.biohackrxiv.org/tag/SWAT4HCLS26
Use the hashtag to post your progress and have it show up on the BioHackRxiv #fediwall: https://guide.biohackrxiv.org/fediwall/
#swat4hcls26
Use the hashtag to post your progress and have it show up on the BioHackRxiv #fediwall: https://guide.biohackrxiv.org/fediwall/
#swat4hcls26
new blog: "All BioHackrXiv preprints and BioHackathon RSS feeds" https://doi.org/10.59350/18gr7-6mx88
"One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed […]
[Original post on social.edu.nl]
"One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed […]
[Original post on social.edu.nl]
June 22, 2025 at 2:18 PM
new blog: "All BioHackrXiv preprints and BioHackathon RSS feeds" https://doi.org/10.59350/18gr7-6mx88
"One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed […]
[Original post on social.edu.nl]
"One thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed […]
[Original post on social.edu.nl]
LLM and knowledge graphs using BioCypher and BioChatter for Plant Data Integration
Versailles, France - 12 to 15 Nov 2024
BioHackrXiv publication in early 2025.
Aknowledgment
ELIXIR staff exchange scheme, ELIXIR-de and Joint Linkage Call NARO-INRAE. @urgi-inrae.bsky.social
Versailles, France - 12 to 15 Nov 2024
BioHackrXiv publication in early 2025.
Aknowledgment
ELIXIR staff exchange scheme, ELIXIR-de and Joint Linkage Call NARO-INRAE. @urgi-inrae.bsky.social
November 22, 2024 at 10:54 AM
LLM and knowledge graphs using BioCypher and BioChatter for Plant Data Integration
Versailles, France - 12 to 15 Nov 2024
BioHackrXiv publication in early 2025.
Aknowledgment
ELIXIR staff exchange scheme, ELIXIR-de and Joint Linkage Call NARO-INRAE. @urgi-inrae.bsky.social
Versailles, France - 12 to 15 Nov 2024
BioHackrXiv publication in early 2025.
Aknowledgment
ELIXIR staff exchange scheme, ELIXIR-de and Joint Linkage Call NARO-INRAE. @urgi-inrae.bsky.social
#SWAT4HCLS starts Feb 24 At the #Biohackathon, I’d like to explore how #Pandoc, #Myst, #JupyterBook can generate RDF and SPARQL-driven reports while also supporting ontology maintenance and hosting.
Inspired by #Biohackrxiv, which uses GitHub & Pandoc.
www.linkedin.com/posts/andra-...
Inspired by #Biohackrxiv, which uses GitHub & Pandoc.
www.linkedin.com/posts/andra-...
Andra Waagmeester on LinkedIn: Barcelona 2025
#SWAT4HCLS 2025 kicks off on February 24th! Expect a full week of tutorials, conference talks, and the #Biohackathon!
📅 The Biohackathon will be the last day…
www.linkedin.com
February 15, 2025 at 12:31 PM
#SWAT4HCLS starts Feb 24 At the #Biohackathon, I’d like to explore how #Pandoc, #Myst, #JupyterBook can generate RDF and SPARQL-driven reports while also supporting ontology maintenance and hosting.
Inspired by #Biohackrxiv, which uses GitHub & Pandoc.
www.linkedin.com/posts/andra-...
Inspired by #Biohackrxiv, which uses GitHub & Pandoc.
www.linkedin.com/posts/andra-...
@biohackrxiv btw. this preprint lists precious few references. Of course, since it is a mainly a description of software items (issues, bug fixes, new features). BUT all references show modest citation ontology references, too!
April 27, 2026 at 7:28 PM
@biohackrxiv btw. this preprint lists precious few references. Of course, since it is a mainly a description of software items (issues, bug fixes, new features). BUT all references show modest citation ontology references, too!
the first four #bh25jp preprints have appeared in BioHackRxiv: https://index.biohackrxiv.org/
This includes "Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1 and "A Lightweight PURL Resolver for Linked Life Science Data" […]
This includes "Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1 and "A Lightweight PURL Resolver for Linked Life Science Data" […]
Original post on mastodon.social
mastodon.social
October 4, 2025 at 9:23 AM
the first four #bh25jp preprints have appeared in BioHackRxiv: https://index.biohackrxiv.org/
This includes "Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1 and "A Lightweight PURL Resolver for Linked Life Science Data" […]
This includes "Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1 and "A Lightweight PURL Resolver for Linked Life Science Data" […]
no, no, and no. Context in narratives matter.
October 12, 2025 at 6:38 AM
no, no, and no. Context in narratives matter.
RE: https://fediscience.org/@biohackrxiv/116268226414358068
Need to look this up: SWAT4HCLS ➡️ "Semantic Web Application and Tools for Health Care and Life Sciences" 😉
Personally, I am a little sceptic when it comes to web applications and reproducibility. So, I will try to stay open-minded […]
Need to look this up: SWAT4HCLS ➡️ "Semantic Web Application and Tools for Health Care and Life Sciences" 😉
Personally, I am a little sceptic when it comes to web applications and reproducibility. So, I will try to stay open-minded […]
March 21, 2026 at 5:05 PM
RE: https://fediscience.org/@biohackrxiv/116268226414358068
Need to look this up: SWAT4HCLS ➡️ "Semantic Web Application and Tools for Health Care and Life Sciences" 😉
Personally, I am a little sceptic when it comes to web applications and reproducibility. So, I will try to stay open-minded […]
Need to look this up: SWAT4HCLS ➡️ "Semantic Web Application and Tools for Health Care and Life Sciences" 😉
Personally, I am a little sceptic when it comes to web applications and reproducibility. So, I will try to stay open-minded […]
Another good year for explicit CiTO annotations! https://scholia.toolforge.org/cito/
Thanks to all Journal of Cheminformatics and BioHackrXiv authors!!!
Looking forward to the #bh25eu and #bh25de preprints with CiTO annotations! Help us set a new record ;) […]
[Original post on mastodon.social]
Thanks to all Journal of Cheminformatics and BioHackrXiv authors!!!
Looking forward to the #bh25eu and #bh25de preprints with CiTO annotations! Help us set a new record ;) […]
[Original post on mastodon.social]
October 12, 2025 at 6:47 AM
Another good year for explicit CiTO annotations! https://scholia.toolforge.org/cito/
Thanks to all Journal of Cheminformatics and BioHackrXiv authors!!!
Looking forward to the #bh25eu and #bh25de preprints with CiTO annotations! Help us set a new record ;) […]
[Original post on mastodon.social]
Thanks to all Journal of Cheminformatics and BioHackrXiv authors!!!
Looking forward to the #bh25eu and #bh25de preprints with CiTO annotations! Help us set a new record ;) […]
[Original post on mastodon.social]
@essepuntato, I just filed a request for an additional CiTO ontology term: "is inspired by"
https://github.com/SPAROntologies/cito/issues/12
https://github.com/SPAROntologies/cito/issues/12
"is inspired by" · Issue #12 · SPAROntologies/cito
I like to request an addition CiTO citation intent: is inspired by. Example: The Journal of Open Source Software (Smith et al., 2018) was the original inspiration for BioHackrXiv. I can imagine thi...
github.com
September 18, 2026 at 9:43 AM
@essepuntato, I just filed a request for an additional CiTO ontology term: "is inspired by"
https://github.com/SPAROntologies/cito/issues/12
https://github.com/SPAROntologies/cito/issues/12
@tschfflr honestly? I only published one preprint with them. This year. Via @biohackrxiv. No idea what an #OpenScience workflow with OSF looked like. 🤷♂️
Wish there would be more consensus between the disciplines.
Wish there would be more consensus between the disciplines.
August 11, 2026 at 7:44 PM
@tschfflr honestly? I only published one preprint with them. This year. Via @biohackrxiv. No idea what an #OpenScience workflow with OSF looked like. 🤷♂️
Wish there would be more consensus between the disciplines.
Wish there would be more consensus between the disciplines.