#Biohackrxiv
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biohackrxiv.fediscience.org.ap.brid.gy
our preview website has been revamped: https://preview.biohackrxiv.org/

#biohackrxiv #preprint #biohackathon
New website (see link from main post). It shows in the left column the BioHackrXiv "BHX" logo with short explanation what BHX is. On the right is the new content. Users no longer have to select a BioHackathon, but all that information is now extracted from the paper.md itself. The "Getting Started" box explains the process. Under this box is now only the two options to provide the paper, Option 1 being the repository URL, and the Option 2 is to upload a .zip file.
November 4, 2025 at 2:39 PM
biohackrxiv.fediscience.org.ap.brid.gy
hi, this is the Mastodon account for the BioHackrXiv preprint server! We will be posting new preprints via this account

#introduction
November 3, 2025 at 4:56 PM
europepmc.org
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
Europe PMC includes preprints from 34 preprint servers. Including: Access Microbiology, AfricArXiv, agriRxiv, AIJR Preprints , ARPHA, Preprints , arXiv, Authorea Preprints, Beilstein Archives, BioHackrXiv, bioRxiv, ChemRxiv , EcoEvoRxiv, Emerald Open Research, F1000 Research, Gates Open Research, Health Open Research, HRB Open Research, MedEdPublish, medRxiv, MetaArXiv, NIHR Open Research, Open Research Africa, Open Research Europe, PaleorXiv, PeerJ Preprints , Preprints.org, PsyArXiv, Qeios, Research Square, SciELO Preprints, ScienceOpen Preprints, SSRN, VeriXiv, and Wellcome Open Research.
October 24, 2025 at 12:25 PM
egonw.mastodon.social.ap.brid.gy
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]
Screenshot of the "Number of articles with CiTO-annotated citations by year" panel, showing articles with explicit CiTO annotations (so, as part of the articles themselves!), first in 2010 (you should know that by now), and then Journal of Cheminformatics preprints since 2020 (3, 8, 5, 4, 2, 2, yeah, not increasing) and BioHackrXiv since 2022 (2, 11, 13, 10). With BioHackathon Europe and BioHackathon Germany still taking place, we should be able to set a new high.
October 12, 2025 at 6:47 AM
egonw.social.edu.nl.ap.brid.gy
no, no, and no. Context in narratives matter.
Screenshot of the "Exploring Bioinformatics in the Wild: Insights from Real LLM Conversations" preprint at BioHackrXiv. In the right sidebar we see textmined annotations: GPT -> Gene/Protein LLama -> Organism Mistral -> Chemical
October 12, 2025 at 6:38 AM
egonw.mastodon.social.ap.brid.gy
@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
Screenshot of the linked page, showing the right collection logo, but the number of items in the collections is not okay. And the first two results are indeed not BioHackrXiv preprints. Something seems to go wrong with the the filtering.
October 12, 2025 at 5:31 AM
egonw.social.edu.nl.ap.brid.gy
I "added" DOI support to the BioHackrXiv Index, so that I now can extract DOIs from preprints and put them in the index. With CiTO annotation that also shows up in the JSON feed :) For example, for this #bh25jp preprint https://doi.org/10.37044/osf.io/8kap3_v1 this looks like this […]
Original post on social.edu.nl
social.edu.nl
October 5, 2025 at 7:34 AM
egonw.mastodon.social.ap.brid.gy
did you know you can follow new preprints in #biohackrxiv?

RSS feed: https://index.biohackrxiv.org//feed.xml

JSON feed: https://index.biohackrxiv.org//feed.json

#preprint #biology
October 4, 2025 at 10:07 AM
egonw.mastodon.social.ap.brid.gy
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" […]
Original post on mastodon.social
mastodon.social
October 4, 2025 at 9:23 AM
egonw.social.edu.nl.ap.brid.gy
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 of the two screenshots of the linked blog post. It shows the "meetings" page, implemented as a tag page, and shows a word cloud of biohackathon shortcodes, at different sizes, following by a Meetings list in reverse chronological order, with two meetings in 2025, and the first five held in 2024.
June 22, 2025 at 2:18 PM
egonw.social.edu.nl.ap.brid.gy
and with that, we also gained 3 new nanopublication, with the oldest discussed articles now in 1977 and 1978. More here: https://scholia.toolforge.org/cito/
Histogram showing non-data set sources of citation intent annotations, with in blue annotations from BioHackRxiv, green from the Journal of Cheminformatics, one in orange from the Journal of Biomedical Semantics, and yellow from the nanopubs. Two more (red and purple) are from two preprints.
June 22, 2025 at 10:19 AM
library.cmu.edu
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...
Participant in the hackathon in March at CMU
June 9, 2025 at 2:49 PM
egonw.mastodon.social.ap.brid.gy
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/
BioHackrXiv Preprints
Preprints for BioHackathons
egonw.github.io
May 29, 2025 at 12:10 PM
tijmen.globalcampus.ai
There's actually three locations in OpenAlex:
api.openalex.org/works/W31319...
OSF, HAL and BioHackrXiv. Not sure though why they're in that order.
api.openalex.org
May 7, 2025 at 9:39 AM
egonw.mastodon.social.ap.brid.gy
hi @OpenAlex, I was just looking at https://openalex.org/works/w3131971476 and do not see where it was published. It was published in #biohackrxiv but do not see that anywhere. it's a preprint server, so, I was wondering how to get BioHackrXiv known to OpenAlex? cc @pjotrprins
OpenAlex (@OpenAlex@mastodon.social)
229 Posts, 0 Following, 1.33K Followers · OpenAlex is an open index of the global research system. Made with ❤️ by @OurResearch_org.
mastodon.social
May 7, 2025 at 9:07 AM
egonw.social.edu.nl.ap.brid.gy
very exciting that the Journal of Cheminformatics (jcheminf.biomedcentral.com@rss-parrot.net) authors continue to submit CiTO annotation :) https://doi.org/10.1186/s13321-025-01009-0

That brings it to 24 journal articles and 35 preprints. I have updated the […]

[Original post on social.edu.nl]
Scholia CiTO page panel for "Number of articles with CiTO-annotated citations by year", with 7 bars, representing the years 2010 and 2020-2025. Green is the Journal of Cheminformatics, peaking in 2021 with 8 articles, and Blue is the BioHackrXiv, peaking (so far) in 2024, with 13 preprints.
April 29, 2025 at 9:21 AM
europepmc.org
🔍 #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
Image of logos of preprints servers indexed in Europe PMC. Logos are of the following preprint servers: Access Microbiology, AfricArXiv, agriRxiv, AIJR Preprints, ARPHA Preprints, arXiv, Authorea Preprints, Beilstein Archives, BioHackrXiv, bioRxiv, ChemRxiv, EcoEvoRxiv, Emerald Open Research, F1000 Research, Gates Open Research, Health Open Research, HRB Open Research, MedEdPublish, medRxiv, MetaArXiv, NIHR Open Research, Open Research Africa, Open Research Europe, PaleorXiv, PeerJ Preprints, Preprints.org, PsyArXiv, Qeios, Research Square, SciELO Preprints, ScienceOpen Preprints, SSRN, VeriXiv, and Wellcome Open Research.
April 29, 2025 at 8:10 AM
hkanekane.bsky.social
BioHackrXivにハッカソンやワークショップの成果をまとめて、形にするのは大切

BioHackrXivの担当者の皆様、ありがとうございました
March 14, 2025 at 10:15 PM
egonw.social.edu.nl.ap.brid.gy
new report/preprint: "BioHackEU24 report: @ORCID_Org and @ResearchOrgs identifiers in BioHackrXiv reports" https://doi.org/10.37044/osf.io/p9u42_v1

"As part of the BioHackathon Europe 2024, we here report on two improvements of theplatform: visualization of the ORCID identifiers in the […]
Original post on social.edu.nl
social.edu.nl
March 11, 2025 at 8:52 AM
andrawaag.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-...
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
egonw.mastodon.social.ap.brid.gy
the two most cited #biohackrxiv papers are:

- "ELIXIR Software Management Plan for Life Sciences", by Renato Alves et al., 2021, https://doi.org/10.37044/osf.io/k8znb
- "Connecting molecular sequences to their voucher specimens", by Quentin Groom et al., 2021, https://doi.org/10.37044/osf.io/93qf4
OSF
osf.io
February 9, 2025 at 9:05 AM
egonw.mastodon.social.ap.brid.gy
congrats to #biohackrxiv with their 100th preprint! https://osf.io/preprints/biohackrxiv/discover?sort=-dateCreated

#openscience #hackathon #biohackeu24 #biohackjp24 #biohackgermany24
Screenshot of the BioHackrXiv page listing the 100 preprints, showing the logo made of the letters B, H, and X (a bit like a wooden block B, and the H and X made of shelfs), a search bar, the text "100 results" and then the titles of the three latest preprints: - "BioHackGermany24 report: User-friendly ISA-based metadata annotation of life science experiments with ISA Wizard", by Patrick König and Sebastian Beier, on Feb 7 - "BioHackJP24 report: Running a WikiBlitz", by Andra Waagmeester , Shuya Ikeda , Yasunori Yamamoto , Erick Antezana , Núria Queralt Rosinach , and 1 more, on Feb 5 - "BioHackEU24 report: Bioschemas for Mortals", by Nick Juty , Phil Reed , and Helena Schnitzer, on Feb 2
February 9, 2025 at 6:48 AM
egonw.mastodon.social.ap.brid.gy
and the first 2025 paper with explicity CiTO annotations to make a FAIR statement about why an article is cited is a fact! "BioHackEU24 report: Bioschemas for Mortals" https://doi.org/10.37044/osf.io/dch6w

See https://scholia.toolforge.org/cito/

#fair #openscience #wikidata
Histogram showing the number of papers (journal articles + preprint) with explicit CiTO annotation in the article itself. Bigger providers are the Journal of Cheminformatics (green) and BioHackrXiv (blue). The oldest paper is from 2010, then the first next three in 2020, and this week the first in 2025. The peak so far was 2023 with 16 articles, followed by 2024 with 15.
January 31, 2025 at 11:19 AM
egonw.mastodon.social.ap.brid.gy
nice to see the first #biohackrxiv 2025 paper with Citation Typing Ontology (CiTO) annotation: "Enhancing multi-omic analyses through a federated microbiome analysis service" https://scholia.toolforge.org/work/Q131798238 https://doi.org/10.37044/osf.io/3x274

BioHackRxiv […]
Original post on mastodon.social
mastodon.social
January 18, 2025 at 12:46 PM
stephenturner.us
Enhancing multi-omic analyses through a federated microbiome analysis service https://osf.io/preprints/biohackrxiv/3x274 #Nextflow 🧬🖥️🧪
January 10, 2025 at 7:30 PM