Curious how your #Fediverse instance has been doing in 2025, in terms of activity? Check out https://fedidb.com/servers/ 2025 has been a good year for social.edu.nl 😻😻 @SLURF @SURF 😻😻 And we have some plans to make it do even better next year. More about this […] [Original post on social.edu.nl]

new blog post: "Rescuing @wdscholia #2: getting closer" https://chem-bla-ics.linkedchemistry.info/2025/12/31/rescuing-scholia-2-getting-close.html https://doi.org/10.59350/6t2qh-2f839 "But we are getting close. So, please give qlever.scholia.wiki a go, and let us know your observations. As […]

My first time ever on this list 😉 . While I don't like gamification, it is certainly something I couldn't miss today when cleaning tabs. #nanopub #gamification

new blog post: "Open Infrastructures #1: Research Software Directory" https://chem-bla-ics.linkedchemistry.info/2025/12/29/open-infrastructures.html https://doi.org/10.59350/g30ef-gxm10 "RSD gives rich context to the research software. It can track the […] [Original post on social.edu.nl]

As Hanukkah commenced on December 25th, it seems like a perfect opportunity to revisit a previous Lipid of the Month (#LoM) from earlier this year: Triolein. Check it out at lipidmaps.org/updates/lipi...

new blog post: "Open Infrastructures #1: Research Software Directory" https://chem-bla-ics.linkedchemistry.info/2025/12/29/open-infrastructures.html https://doi.org/10.59350/g30ef-gxm10 "RSD gives rich context to the research software. It can track the […] [Original post on social.edu.nl]

congrats to @wikidata for passing the 120M items! https://www.wikidata.org/wiki/Wikidata:Main_Page #wikidata

Today we are calling on institutions around the world to take control of their #digitalsovereignty, including their social accounts. Governments should communicate directly with their citizens on open platforms, not through the mouthpiece of a corporation […]

"The TRIPOD-LLM reporting guideline for studies using large language models" https://doi.org/10.1038/s41591-024-03425-5 "We present transparent reporting of a multivariable model for individual prognosis or diagnosis (TRIPOD)-LLM, an extension of the TRIPOD + artificial intelligence statement […]

🥳 Guinea and Kenya eliminated sleeping sickness. 🥳 Niger became the first African country to eliminate river blindness. 🥳 Georgia, Suriname and Timor-Leste were certified malaria-free. 🥳 Brazil eliminated mother-to-child transmission of #HIV. 🔗 bit.ly/49wdcpl

RE: https://mastodon.social/@egonw/115762868178809191 nog iets meer dan 60 minuten te gaan #sr25

it has been a busy yea. Aren't they all? Yes, but 2025 was exceptional. Do I have evidence? Yes, severe dip in the number of published journal articles this year. That happened once before (2008). But, journal article counts remain a, umm, limited metric of research output. So much important […]

December 2025 WikiPathways release: 840 edits by 8 contributors and 9 new pathways. Accessible via #webservices, #rstats, #PathVisio and #Cytoscape. https://www.wikipathways.org/#download #bioinformatics #elixirnl

Hype. No form of CO₂ removal is a climate solution as long as we’re still releasing >40 billion tonnes of CO₂ every year from fossil fuel burning. https://www.winnipegfreepress.com/breakingnews/2025/12/19/hope-or-hype

Euclid 2.14 is released: https://doi.org/10.5281/zenodo.17996224 https://github.com/BlueObelisk/euclid/releases/tag/euclid-2.14 Minor update with upgraded dependencies to Log4j 2.25.3 and Commons IO 2.21 and Lang3 3.20. Euclid is a library of numeric, geometric and XML routines. #java […]

🌐🌱🌐 PlantMetWiki is live! 🌐🌱🌐 A linked open data service for querying and analyzing plant pathway knowledge. Plants are incredibly rich in chemistry, but knowledge about their biosynthesis is scattered across databases, tools, and publications. #plantmetwiki brings this knowledge together ➡️ […]

"Overall, our findings show that Wikipedia offers both a chemically diverse and socially informative perspective on molecules, making it a unique resource at the intersection of chemistry, open data, and public knowledge." https://doi.org/10.1021/acs.jcim.5c02538.s001 With 22k SMILES in a […]

former BiGCaT colleague Serena Bonaretti has written the #openaccess book about #python: "Learn Python with Jupyter", now available from various stores and online at https://www.learnpythonwithjupyter.com/

"MCP server tools with RDF shapes" https://doi.org/10.37044/osf.io/8qeh5_v1 "In this paper, we present the work we have done during the Japan Biohackathon 2025 about implementing MCP servers supported by RDF data shapes to improve natural language interactions with large RDF datasets using […]

RE: https://vis.social/@infobeautiful/115719202661538129 any interesting conferences in Spain in August 2026?

@wikipathways @egonw Next attempt. Just using these libs: library(rWikiPathways) library(XML) library(dplyr) library(igraph) library(ggraph) library(ggplot2) Still need to polish and work on the colour scale, though. Honestly? I, considering my workload, I […] [Original post on fediscience.org]

Has anybody else noticed the COD server appears to be down. No, I don't mean "Call of Duty". https://www.crystallography.net/

The hidden health risks of bottled water https://theconversation.com/the-hidden-health-risks-of-bottled-water-268513 Growing mistrust of tap water has helped turn bottled water into a global staple, even in countries where public supplies are among the most rigorously tested. Marketing has […]

"A noteworthy finding is that the identities of many chemicals remain publicly unknown because they are claimed as confidential (over 50 000) or ambiguously described (up to 70 000)." https://pubs.acs.org/doi/10.1021/acs.est.9b06379

PCI Statistics and Machine Learning (@PCI_StatML) is now open for submissions!! https://statml.peercommunityin.org/ For an updated list of all the thematic PCIs, visit https://peercommunityin.org/current-pcis/

new blog: "Rescuing Scholia: will we make it in time?" https://doi.org/10.59350/yh369-rr787 https://chem-bla-ics.linkedchemistry.info/2025/12/08/rescuing-scholia.html "What started out in 2016 on Twitter became a (small) award winning decade long collaborative project. Unfortunately, the future […]

"The first rule of research integrity is always cite your sources." From "Reference checks in Oversight" https://doi.org/10.59350/7ax4r-hk815 Nice blog post about citation practices, retractions, and citation networks.

got GPML files on @github? Validate them with this action: jobs: test: name: "Validate XSD files" runs-on: ubuntu-latest steps: - name: Checkout uses: actions/checkout@v6 - name: Validate XSD files conform to the specs uses: phpcsstandards/xmllint-validate@v1 with: pattern: "pathways/*.gpml" […]

Surf zoekt zo’n tweeduizend docenten, onderzoekers en andere medewerkers die Nextcloud willen uitproberen, een serieus Europees alternatief voor Microsoft. dub.uu.nl/nl/nieuws/su...

@egonw a few days ago, I updated bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package! Today, after quite some tinkering, I managed to overly differential expression results. This is not stable code, yet. The […] [Original post on fediscience.org]

Don’t forget to register for this month’s LIPID MAPS #webinar with James Olzmann, titled ‘Cellular lipid homeostasis: From lipid droplets to ferroptosis’. Register now: zoom.us/webinar/regi...

RE: https://social.edu.nl/@tgx_um/115645028833529913 on Monday we have a go/no-go and we really want to go So, are you considering sign up before Sunday evening! #ontologies #linkeddata #sparql

There’s still time to register for TODAY’s FREE online #BeilsteinTalk “The value of data-sharing for reaction discovery and development” with Simon Coles and Sally Bloodworth, University of Southampton. 📅 Dec 4, 2025 🕒 3–4 pm CET 🔗 […] [Original post on hessen.social]

‼️ La invasión de satélites como Starlink también arruinará las imágenes del Hubble y otros telescopios espaciales www.eldiario.es/1_c38a03?utm...

getting ready for (already) the 7th #vhp4safety #hackathon! VHP4Safety is NWO-funded research project, co-creating a virtual human (platform) to host digital twins, to support toxicology research and risk assessment. Why? to replace as much as possible, if not all, animal testing. And the […]

NUTRIM Open Science: "In our series on open science, this edition features Mireille Sthijns and Cynthia Ly, highlighting their contributions to our community and their dedication to transparency and accessibility—not only for fellow researchers but for society at large." […]

🚀 BioSB course "Knowledge Graphs in the Life Sciences” 🚀 Don't miss this exciting opportunity for Life Sciences researchers and data enthusiasts. In just 9 weeks, BioSB will host this course: https://www.dtls.nl/courses/knowledge-graphs-in-the-life-sciences-2026/ 📅 January 5–9, 2025 🗺️ […]

new blog: "WikiPathways curation reports on profile pages" https://doi.org/10.59350/s7vw2-r7y02 https://chem-bla-ics.linkedchemistry.info/2025/11/30/wikipathways-curation-reports-on-profile-pages.html #bioinformatics #cheminformatics #curation

Chernobyl Fungus Appears to Have Evolved an Incredible Ability https://www.sciencealert.com/chernobyl-fungus-appears-to-have-evolved-an-incredible-ability That fungus is called Cladosporium sphaerospermum, and some scientists think its dark pigment – melanin – may allow it to harness ionizing […]

new blog: "WikiPathways curation reports on profile pages" https://doi.org/10.59350/s7vw2-r7y02 https://chem-bla-ics.linkedchemistry.info/2025/11/30/wikipathways-curation-reports-on-profile-pages.html #bioinformatics #cheminformatics #curation

@wikipathways still has a good number (200 to 250) pathways that do not have a single reference (which does not mean no references were used): https://www.wikipathways.org/wikipathways-collection/index2#at-least-one-reference I think we need some gamification here... a few tools that take the […]

TIL I actually did (well, experimented with) preregistration 10 years go: https://web.archive.org/web/20150119044816/http://onsnetwork.org/chemblaics/ 2015: "Open Notebook Science] Network supports researchers of all disciplines. We believe the world can benefit from access to all knowledge. If […]

oh, nice to see the eNanoMapper database paper (https://doi.org/10.3762/bjnano.6.165) got a mention in Wikipedia :) https://acs.altmetric.com/details/4332183/wikipedia

The submission deadline for the ICCS Collection in the Journal of Cheminformatics will be extended to March 1. We currently have four papers under review and expect at 2 more submissions. https://link.springer.com/collections/jcfcedbfda #cheminformatics #iccs2025

I'm wondering: If a published paper mentions that a study was approved by the ethics committee of University X, number XXXX, is there a way to find (and read) this ethics approval? #metascience #ethics #academia

"‘This is censorship.’ Conference requires abstracts to comply with Trump anti-DEI order." https://www.science.org/content/article/censorship-conference-requires-abstracts-comply-trump-anti-dei-order "Planetary scientists planning to attend a prominent conference may soon face a difficult […]

On 15 December 2025, the Open Science Community Maastricht (OSCM) is hosting a hands-on workshop by Roman Briker: “Pre-registration: Why, How, and Where?” Pre-registration is one of the key steps toward making research more transparent, trustworthy, and […] [Original post on social.edu.nl]

Musk hat in X die Standortinformationen der Nutzer frei gegeben. Es zeigt sich, die mit Abstand meisten MAGA-Accounts sitzen in Nordafrika und Indien bzw auf der arabischen Halbinsel! www.thecanary.co/trending/202...