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Egon Willighagen

@egonw.social.edu.nl.ap.brid.gy
491 followers 12 following 518 posts

This account is used for tooting conferences and about the Dutch academic system. Sometimes Dutch. Toots are personal and searchable. he/him 🌉 bridged from ⁂ social.edu.nl/@egonw, follow @ap.brid.gy to interact

PostsRepliesMedia
Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 3h
als je dat nog niet gedaan hebt, ja, gauw doen. het gaat om shell toegang, dus echt foute boel.
nrc.social
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ICCS @intconfchemstr.social.edu.nl.ap.brid.gy · 8h
in the background, we have started working on the next ICCS conference, to be held in 2028 Just that you know we haven't forgotten about you! #cheminformatics #ICCS2028
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 19/10/2026
@brembs thanks! interesting and important points
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Björn Brembs @brembs.mastodon.social.ap.brid.gy · 19/10/2026
@egonw I'd say that by now the pendulum might have swung in the other direction: you have people who oppose APC-OA because of the payments the authors have to pay, plus those who are opposed to their articles being used to train LLMs. I wouldn't be surprised if OA today is less popular than […]
mastodon.social
Original post on mastodon.social
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 19/10/2026
"The Cost of Knowledge" (http:// thecostofknowledge.com/) exists 15 years next year. Would be nice if we could break the 25k signatures. Who wants to help out? Sign now and/or post your signature with the hashtag. Let's give it a boost and celebrate the new norm #theCostOfKnowledge
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026
new blog: "Peer reviewed articles about biological processes in WikiPathways" chem-bla-ics.linkedchemistry.info/2… #openscience #wikipathways #biology #academicchatter "Earlier this year I […] [Original post on social.edu.nl]
Screenshot of the References section of the linked blog post, with the names highlighted of the "Journal of Cell Communication and Signaling" in yellow, which shows that it by far is the most popular journal (7/12 of the references visible in the screenshot) to publish pathways in WikiPathways in.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026
new blog: "Peer reviewed articles about biological processes in WikiPathways" chem-bla-ics.linkedchemistry.info/2… #openscience #wikipathways #biology #academicchatter "Earlier this year I […] [Original post on social.edu.nl]
Screenshot of the References section of the linked blog post, with the names highlighted of the "Journal of Cell Communication and Signaling" in yellow, which shows that it by far is the most popular journal (7/12 of the references visible in the screenshot) to publish pathways in WikiPathways in.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 18/10/2026
new preprint: "Ontology-Driven Annotation of Key Events Enables Transcriptomics-Based Assessment of Adverse Outcome Pathway Networks" doi.org/10.64898/2026.10.06.756965 "We then applied this approach to pesticide-induced hepatotoxicity, using Open TG-GATEs transcriptomics data from […]
social.edu.nl
Original post on social.edu.nl
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026
today I finished migration 2010 of my old blog to my new blog: chem-bla-ics.linkedchemistry.info/a…
chem-bla-ics.linkedchemistry.info
2010
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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FAIR4ChemNL @fair4chemnl.social.edu.nl.ap.brid.gy · 17/10/2026
last week we met with @NFDI4Cat in Frankfurt at the nice DECHEMA offices. We presented the current state of our project, including two posters. One poster is archived here: zenodo.org/records/23364233
Group picture of ~20 people from the FAIR4ChemNL, NFDI4Cat, and NFDI4Chem projects. The group is standing on the stairs in front of the DECHEMA entrance we can see in the background. On the left is a NFD4Cat banner.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026
so, the CC-BY license allows this. What is preventing people from making KEGG pathways available as CC-BY? pmc.ncbi.nlm.nih.gov/articles/PMC11… Why I am not? 1. the KEGG team decided for a different sustainability model. That is their perfect right. 2. WikiPathways is CCZero so […]
social.edu.nl
Original post on social.edu.nl
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/10/2026
nice guide by @larsgw on how to update your @wikidata SPARQL queries for the upcoming QLever migration of WDQS
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Geoff Hutchison @geoffhutchison.net · 16/10/2026
I'm going to follow up.. #chemsky How do we make chemical structures (either 2D or 3D), reactions accessible to alt-text and screen readers, etc. Do I turn it into a name "this diagram indicates caffeine or 1,3,7-trimethylxanthine" I'd really welcome thoughts and discussion...
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Marije de Vries @marije.social.edu.nl.ap.brid.gy · 15/10/2026
UU-ers opgelet! Er komt weer een Digitale Autonomie Cafe UU aan! Op 2 november tussen 12-14 uur zijn jullie van harte welkom om onder het genot van een broodje aan te sluiten bij interessante sessies over digitale autonomie. We hebben weer een interessant […] [Original post on social.edu.nl]
mensen kijken naar scherm
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 15/10/2026
TIL about the Undiagnosed Hackathon
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Marc van Oostendorp @fonolog.mstdn.social.ap.brid.gy · 15/10/2026
Gisteren vroeg de KNAW – terecht – aandacht voor de academische vrijheid en de vrijheid van meningsuiting door wetenschappers. Pleidooi om een stap verder te gaan, naar een recht op wetenschap. neerlandistiek.nl/2026/10/voor-het-…
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 15/10/2026
Sounds like an interesting read! "Prehistoric global migration of vanishing gut microbes with humans" doi.org/10.1038/s41586-026-11106-1 "Our findings indicate that a diverse gut microbiome co-migrated with humans worldwide and has persisted over millennia."
nature.com
Prehistoric global migration of vanishing gut microbes with humans - Nature
Microbial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.
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Beilstein-Institut @beilsteininstitut.hessen.social.ap.brid.gy · 14/10/2026
No code needed: our open-source tool BChemXtract now has a web interface, BChemXtractWeb. ✅ Extracts structures from CDX/CDXML files ✅ Generates SMILES, InChI, InChIKey, and formula ✅ Links to PubChem ✅ Exports to SDF, Molfile V3000, and JSON 🔗 […] [Original post on hessen.social]
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 14/10/2026
War is a choice. A choice of Putin of Trump. Of others. It is not inevitable, it is not human nature. It is a choice to let people in charge to do not mind to see their other people die
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WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · 11/10/2026
October 2026 WikiPathways update: 30 edits in 45 pathways by 2 contributors, including 12 new pathways and 2 new species (Bombyx mori and Apis cerana): www.wikipathways.org/index.php/Down… #bioinformatics #openscience #opensource More news at […]
fosstodon.org
Original post on fosstodon.org
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 11/10/2026
the possible risks of new scientific knowledge is not limited to natural sciences. Our knowledge about the human brain, our knowledge of society, very much too. Just think political ads. "Encouraging Americans to hate one another is an unfortunate side effect." -- Lieberman and Long
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 11/10/2026
SPARQL endpoints are probably the most dopaminergic API currently existing
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Magnus Manske @magnusmanske.wikis.world.ap.brid.gy · 10/10/2026
The QuickStatements database was by far the largest one on Toolforge, weighing 274GB in mostly one table. I have now archived all jobs older than 3 months, and will continue to do so. If you access an older job, it be transparently loaded back into the database, so nothing changes for you […]
wikis.world
Original post on wikis.world
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 10/10/2026
great example of where we are. After 20 years, we are finally landed: high quality data is essential, we provide an API on top of that, and then any view on top of that is easily made in whatever flavor of use is trivial #bioinformatics #biology
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Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 08/10/2026
It’s simply unimaginable that CDC Director Dr. Erica Schwartz has just bowed to RFK Jr. and approved funding for an utterly unethical clinical trial that will withhold the birth dose of HepB vaccine in Guinea Bissau. It is to be conducted by researchers accused of academic misconduct.
rollingstone.com
CDC Is Moving Forward With a Previously Shelved Controversial Hepatitis B Vaccine Study
“It’s a wholly unethical trial, and it shouldn’t be allowed,” says Dr. Paul Offit of Guinea-Bissau study
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 08/10/2026
For any sufficiently uneducated human, anything remotely magical must be super-intelligent.
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Björn Brembs @brembs.mastodon.social.ap.brid.gy · 06/10/2026
Wonderful new work from Tom Clandinin's lab on how an animal's internal neural activity decides whether to react to external stimuli or to ignore them: "Unique neural activity states predict action selection in response to visual threat" […]
mastodon.social
Original post on mastodon.social
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 05/10/2026
new blog post: "Open Science and Recognition & Rewards" chem-bla-ics.linkedchemistry.info/2… #openscience #recognition #rewards "Now, because open science and team science are used a lot in the Theme Bioinformatics of our Department of […]
social.edu.nl
Original post on social.edu.nl
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 03/10/2026
new blog: "New paper: "ToxTempAssistant: using large language models to standardise cell-based toxicological test method descriptions"" […] [Original post on social.edu.nl]
Screenshot of the acceptance note of the article, as archived on Zenodo by the journal. It shows the publisher code of the submission ("TEBT-2025-0014") and below that a colored table with blue, yellow, and green rows, with various bits of information, including the submission title, handling editor, number of reviewers (3), preprint DOI, evaluation stage, and final recommentation ("Accept").
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 03/10/2026
just saw a book published two weeks ago with a chapter with this title: "Methods of Bioinofrmatics and Chemoinformatics in Drug Dvelopment" The chemoinformatics (with an o) is going strong!
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/10/2026
TIL I learned why I dislike competitions and winning. I hate the dopamine crash that follows.
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LIPID MAPS @lipidmaps.bsky.social · 02/10/2026
😊 Want a reason to smile? Look no further than Anandamide (AEA) = the body's very own "bliss molecule"! This lipid neurotransmitter regulates mood, anxiety, and happiness. Wear a smile today and thank your endogenous lipid signaling! 🧠✨ lipidmaps.org/databases/lm... #WorldSmileDay #LipidMAPS
lipidmaps.org
https://lipidmaps.org/databases/lmsd/LMFA08040001
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/10/2026
TIL about DrugRxiv, a new preprint service for drug repurposing: drugrepocentral.scienceopen.com/col… #openscience #drugDiscovery #chemistry First thoughts: 1. I think these preprints would fit well on ChemRxiv too. 2. nice to see @Science_Open is alive and kicking! 3 […]
social.edu.nl
Original post on social.edu.nl
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 02/10/2026
the Dutch Virtual Human Platform 4 Safety (VHP4Safety) project has a series of webinars upcoming. www.sciencrew.com/c/6594/a/33572695… #toxicology #safety #nederlandseWetenschapsAgenda
"Save the date" infographics for the "VHP4Safety Webinar Series" showing three colored hexagons with the three date/times of the three webinars and next to that the three webinar titles. All on a light blue background. Full details:

Introduction to the VHP
14 October 2026, 13:00 to 14:30 CEST

The first webinar will introduce the VHP4Safety project and the Virtual Human Platform. Participants will see how the platform works, explore its tools and learn how it can support safety assessment workflows. The programme will include a live demonstration of the platform and an example of how it was used to address a regulatory question related to thyroid hormone-mediated brain development.

Deep dive into the Parkinson's case study
28 October 2026, 13:00 to 14:30 CET

The second webinar will focus on VHP4Safety’s Parkinson’s case study. Speakers will explain how the Virtual Human Platform brings together in vitro research, Adverse Outcome Pathways, experimental data and available methods to support risk assessment, as demonstrated through the Parkinson’s case study.

From innovation to implementation
18 November 2026, 13:00 to 14:30 CET

The final webinar of the VHP4Safety webinar series will focus on the social side of building the VHP, including user research supporting the development and implementation of the Virtual Human Platform. It will also examine the public acceptance of computational models and artificial intelligence in risk assessment. The webinar will show how stakeholder needs and perspectives can support the development of tools that are scientifically robust, transparent and fit for purpose.
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Avogadro Project @avogadro.cc · 01/10/2026
What's this? Avogadro2 in a web browser?! #compchem #opensource #prototype
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Nessa Carson @supersciencegrl.co.uk · 30/09/2026
Sadly my Sichuan peppercorns (a little expired...) are no longer giving that lovely mala effect :( they still add some flavour but that's about it so I guess I need new spice. Here's the compound allegedly responsible for the effect; I wonder what it's degraded to? en.wikipedia.org/wiki/Hydroxy...
en.wikipedia.org
Hydroxy-α-sanshool - Wikipedia
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Nessa Carson @supersciencegrl.co.uk · 01/10/2026
Yes ACS it's called writing a citation-dense section of a publication 🙄 I guess JOC is off-limits for hopefully just a few minutes...
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Nessa Carson @supersciencegrl.co.uk · 01/10/2026
Looooool I've only seen this written as "canonicalized" before Canonized SMILES strings sounds more like a @chemscrapes.bsky.social cartoon! 👼
Screenshot from a paper. Text: 
"To ensure consistency and accuracy in representing these metabolic molecules, each molecule was represented by its SMILES string. The SMILES strings recovered from PubChem were canonized using Indigo python package, ensuring a standardized description of the molecular structures [27]."
The word "canonized" is highlighted.
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petersuber @petersuber.fediscience.org.ap.brid.gy · 27/09/2026
In March 2025, #Oxford announced that it was working with #OpenAI to digitize #PublicDomain #books from the #BodleianLibrary. www.bodleian.ox.ac.uk/about/media/o… The announcement says that the digitized works "will become searchable and accessible for students and […]
fediscience.org
Original post on fediscience.org
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 27/09/2026
should we not be "Retracting datasets?" chem-bla-ics.linkedchemistry.info/2… doi.org/10.59350/x7zsv-0c792 #data #openscience "A bit over half a year ago, Markus Englund wrote about copy/paste errors in scientific datasets. I believe that many of […]
social.edu.nl
Original post on social.edu.nl
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Egon Willigh☮gen 🟥 @egonw.mastodon.social.ap.brid.gy · 26/09/2026
made some small improvements to my blog: chem-bla-ics.linkedchemistry.info - both mastodon accounts now show up - d3.js word cloud on tags page (finally) - blog post level JSON - references are now cached server side - better pagination
The tags page now has the top tags as a word cloud, and the rest as a list under "more tags". The most abundant tag is "cdk" followed by "bioclipse". The cloud color scheme is shades of orange and grey.
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WHO @who.int · 25/09/2026
As of 23 September 2026, #DRC has reported 7890 confirmed cases, including 3799 deaths, with a case fatality ratio of 48.1%. Read the full disease outbreak news: bit.ly/4yfSZ1U
Ebola disease caused by Bundibugyo virus - Democratic Republic of the Congo
25 September 2026
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FAIR4ChemNL @fair4chemnl.social.edu.nl.ap.brid.gy · 25/09/2026
so far, we have been using @elixir_europe's TeSS and the @SURF's taxila.nl for sharing events and (training) materials. Because both can scrape the content using community standards like Bioschemas, we now have a GitHub Pages website […] [Original post on social.edu.nl]
Screenshot of the linked page. At the top we see FAIR4ChemNL logo (title + 7 hexagons (benzenes) colored orange, green, and purple. Then follows the page title "FAIR4ChemNL selected events and training materials" and links to an "events" and an "materials" page. Below that a word cloud, based on keywords with which events and materials are annotated, sized by frequency, and colored randomly in the orange, green, and purple from the project logo. "Cheminformatics" is the most frequent keyword.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 24/09/2026
new blog post: "Green Open Access: where is the index?" chem-bla-ics.linkedchemistry.info/2… #openaccess #openalex #wikidata #openscience "Green Open Access is literature that has been made available […] [Original post on social.edu.nl]
Screenshot of a claudevibed application that shows information about a DOI. Here it shows where I could possible get a free version. It shows "full text" links from Europe PMC, OpenAlex, and CrossRef. Here we see that OpenAlex also found the Maastricht University institutional repository. Example of a green open access version.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 24/09/2026
new blog post: "Green Open Access: where is the index?" chem-bla-ics.linkedchemistry.info/2… #openaccess #openalex #wikidata #openscience "Green Open Access is literature that has been made available […] [Original post on social.edu.nl]
Screenshot of a claudevibed application that shows information about a DOI. Here it shows where I could possible get a free version. It shows "full text" links from Europe PMC, OpenAlex, and CrossRef. Here we see that OpenAlex also found the Maastricht University institutional repository. Example of a green open access version.
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Beilstein-Institut @beilsteininstitut.hessen.social.ap.brid.gy · 24/09/2026
🤔 Ever stared at an InChI string with no idea what it means? We built an open-source, browser-based tool to help you understand that. Draw or upload a molecule and it generates the InChI and InChI Key, color-codes each layer, and explains each part. 🔗 Try it […] [Original post on hessen.social]
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 21/09/2026
did you know you can follow additions to my @ORCID_Org profile here in the fediverse? See @0000-0001-7542-0286
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 20/09/2026
I am also particularly keen on the CiTO/Wikidata integration! Powered by qlever.scholia.wiki/cito and chem-bla-ics.linkedchemistry.info/t…, of course. These two screenshots shows that, in a table and in a d3.js bar-with-tooltip, one for […] [Original post on social.edu.nl]
"CiTO page" for the CDK paper. We see the "Replies" tab with a horizontal bar with various sections of various sizes, mostly in shades of green. The bar section size reflects the number of works with the CiTO intention. Here, for the first CDK paper, "uses method in" with 61 citations is the biggest part. Below the horizontal bar showing the four most abundant CiTO intents.Same tab page, but now for the Wakefield paper. The table shows the top six intention types, with CiTO "disputes" in a good second with 78 works that dispute the Wakefield paper. the horizontal bar shows a good "red" section for "negative" intents, like "disputes". But also fascinating is the large green area too.
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 19/09/2026
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
While the Journal of Cheminformatics was a second journal to have explicit CiTO citation intent annotation, BioHackrXiv is clearly overtaking it in adoption. Details here: https://qlever.scholia.wiki/cito/
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 18/09/2026
we hebben al een eigen lijst van nieuwe functionaliteit en we hebben ook review meetings met partners uit de publieke sector, maar ik zou heel graag ook van anderen horen wat ze er van vinden van platform.vhp4safety.nl Commentaren, vragen, enzovoort, zijn allemaal welkom op […]
social.edu.nl
Original post on social.edu.nl
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