iiinova — where your digital self keeps evolving

Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

Avogadro Project @avogadro.cc · 01/10/2026

What's this? Avogadro2 in a web browser?! #compchem #opensource #prototype

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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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]

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Reposted by Egon Willighagen

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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Reposted by Egon Willighagen

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 · 24/09/2026

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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 · 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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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 18/09/2026

we have our own list of feature request and issues, and we have review meetings with stakeholders, but I would not mind an external, "clean room", peer review of the platform.vhp4safety.nl Comments, questions, etc, all welcome in this issue tracker (and by email) […]

social.edu.nl

Original post on social.edu.nl

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 17/09/2026

it is too much to ask expensive publishers. If you just let me submit as JATS XML.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 15/09/2026

the third #Eurotox2026 day is progressing well. I'm in the "omics for regulatory toxicology" session. The first talk was by Mark Viant about the MTox700+ Metabolite Panel, see doi.org/10.1093/toxsci/kfac007

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Lillian Darby 🏳️‍🌈🏳️‍⚧️ | @lilliandarby.bsky.social · 10/05/2026

“In addition to cartels and Islamist terror groups,..our national (counter terrorism) activities will also prioritize the rapid identification and neutralization of violent secular political groups whose ideology is anti-American, radically pro-transgender, anarchist” edition.cnn.com/2026/05/07/p...

edition.cnn.com

Trump administration now classifies Antifa and left-wing networks among ‘major’ terror groups | CNN Politics

The Trump administration has classified left-wing networks like Antifa among “three major types of terror groups” the US faces, according to a counter-terrorism plan released Thursday.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 14/09/2026

Second #EUROTOX2026 day. Dr Clemens Wittwehr (JRC) opens the session. All about AOPs, the foundation, the experiment, scale, and connect.

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Reposted by Egon Willighagen

Marjolein Tamis @willowpje.mastodon.nl.ap.brid.gy · 13/09/2026

Schrödingers dataretentie

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Reposted by Egon Willighagen

Ionica Smeets @ionica.mathstodon.xyz.ap.brid.gy · 13/09/2026

Herinneren jullie je een (geschreven) interview met een wetenschapper dat je erg goed vond? Ik vraag dit voor een cursus wetenschapsjournalistiek.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 13/09/2026

#eurotox2026 has started. I'm in a packed room on AI technologies in toxicology. Marc Teunis opened the session and now Ferran Sanz is talking about eTOX, eTRANSAFE, and VICT3R

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 11/09/2026

Fwd: "Phosphorylate and Spare Not" www.science.org/content/blog-post/p… "Evolutionarily it’ll be interesting to see if later kinases evolved from this sort of take-no-prisoners class, or if there are separate paths involved."

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 09/09/2026

Fwd: "Benelux Metabolomics Days 2026, 22-23 September" www.aanmelder.nl/beneluxmetabolomic… #bmd2026 #metabolomics "Featuring 8 outstanding keynotes: Erin Baker, @schymane, Arthur David, Melanie Bailey, Kyo Bin Kang, Joleen Masschelein, Maria Fedorova & Gabi Kastenmüller and 22 […]

social.edu.nl

Original post on social.edu.nl

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 09/09/2026

new blog post: "WikiPathways: biological pathways across the species" chem-bla-ics.linkedchemistry.info/2… "So, when this week the article Xenbase: A Guide to the Xenopus Genetics and […] [Original post on social.edu.nl]

Thumbnail of part of a screenshot of a Wikidata Query Service bar chart from the linked blog post showing the number of pathways per species, for the six species with the most pathways. Humas is off the scale (>400 pathways), Cow around 240, Mouse around 210, Rat 125, yeast just over 100, and worm around 55.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 09/09/2026

each time I read "A word of caution is, however, warranted...", written by a scholar... yeah, why did you find the need to write that? what did you see? why are you not also writing what you saw? was it that horrendous?

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 06/09/2026

preparing for #EUROTOX2026. First time, all train to Vienna.

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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 04/09/2026

"Discovering life's directed metabolic (sub)paths to interpret human biochemical markers using the DSMN tool" doi.org/10.1039/d3dd00069a #health #aging #biomarker #wikipathways this paper is not getting the attention is deserves: network biology to […] [Original post on social.edu.nl]

Part if Figure 12A: "Network visualization of aging biomarkers found in blood. (A) Overview of directed shortest path calculations for one of the analyzed datasets (MTBLS265) in this study, where relevant metabolites considered to be biomarkers for aging (high CV30 values) have a diamond shape; round nodes depict metabolites needed for connectivity, and hexagons visualize proteins. The thickness of the arrows between the nodes indicates the occurrence of this reaction in different pathways."

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Dept of Translational Genomics @tgx-um.social.edu.nl.ap.brid.gy · 04/09/2026

Dr Susan Coort was keynote at the NuGOweek 2026 this week: "Connecting the dots: pathways and networks in nutrition research" nugo2026.pan.olsztyn.pl #nutrigenomics #NuGOweek #wikipathways Find more about her research here […] [Original post on social.edu.nl]

Coort on stage in front of one of her slides, showing information about the WikIpathways project.

Photo: All rights reserved, Meike Bünger, Health-RI / ELIXIR-NL.

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FAIR4ChemNL @fair4chemnl.social.edu.nl.ap.brid.gy · 04/09/2026

RE: nfdi.social/@NFDI/117211612761422583 who in NL is using Chemotion ELN? Care to share your experiences? Maybe at the CHAINS meeting later this year? But a blog post would be awesome too! #chemistry #nl #opensource

nfdi.social

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