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#reproducibility

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Charles Tapley Hoyt<p>Most cheminformatics code that uses queries ChEMBL struggles with reproducibility.</p><p>chembl-downloader can help:</p><p>&gt;&gt;&gt; import chembl_downloader as cd<br>&gt;&gt;&gt; df = cd.query("""<br> SELECT chembl_id, pref_name<br> FROM molecule_dictionary<br> WHERE pref_name IS NOT NULL<br>""")</p><p>It's even sneaking its way into <span class="h-card" translate="no"><a href="https://masto.ai/@wpwalters" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>wpwalters</span></a></span> and <span class="h-card" translate="no"><a href="https://mastodon.social/@dr_greg_landrum" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>dr_greg_landrum</span></a></span> blogs :)</p><p>Code/Docs: <a href="https://github.com/cthoyt/chembl-downloader" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/cthoyt/chembl-downl</span><span class="invisible">oader</span></a></p><p>Preprint: <a href="https://arxiv.org/pdf/2507.17783" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">arxiv.org/pdf/2507.17783</span><span class="invisible"></span></a></p><p><a href="https://scholar.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>cheminformatics</span></a> <a href="https://scholar.social/tags/chemoinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemoinformatics</span></a> <a href="https://scholar.social/tags/chembl" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chembl</span></a> <a href="https://scholar.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> <a href="https://scholar.social/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://scholar.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
Harald Klinke<p>Offene KI braucht offene Infrastruktur – auch bei der Entwicklung.<br>Das Projekt f13 auf OpenCode stellt Tools für transparente, reproduzierbare Workflows zur Verfügung – von Modelltraining bis Deployment.<br>Ein Schritt Richtung digitaler Souveränität durch offene Werkzeuge.<br><a href="https://det.social/tags/OpenSourceAI" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenSourceAI</span></a> <a href="https://det.social/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <a href="https://det.social/tags/DigitaleSouver%C3%A4nit%C3%A4t" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DigitaleSouveränität</span></a></p><p><a href="https://gitlab.opencode.de/f13" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">gitlab.opencode.de/f13</span><span class="invisible"></span></a></p>
Technology Tales<p>Docker Desktop for Statisticians revolutionises R use by creating isolated, reproducible environments. This eliminates version conflicts and simplifies setups. With Docker, you run pre-configured R containers, enabling efficient and clean analysis environments. Explore container management to enhance statistical work and ensure easy collaborative sharing. <a href="https://mstdn.social/tags/Docker" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Docker</span></a> <a href="https://mstdn.social/tags/Statistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Statistics</span></a> <a href="https://mstdn.social/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <a href="https://mstdn.social/tags/RStats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>RStats</span></a> <a href="https://www.statology.org/docker-desktop-for-statisticians-running-r-in-containers/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">statology.org/docker-desktop-f</span><span class="invisible">or-statisticians-running-r-in-containers/</span></a></p>
Pete Bachant<p>When you describe the computational methods in your paper without sharing the code and data:</p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://fediscience.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a></p>
Pete Bachant<p>One major cause of the reproducibility crisis is that the way we describe computational methods in research articles has not kept pace with the increase in complexity of the methods themselves. Human language and mathematical formulas are not adequate in many cases.</p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://fediscience.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> <a href="https://fediscience.org/tags/opensource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opensource</span></a></p>
Veit Schiele 🔜 @FrOSCon<p>Karl Popper in The Logic of Scientific Discovery, 1959: ‘Non-reproducible single occurrences are of no significance to science.’</p><p>XKCD in Replication Crisis, 2025: ‘Replication Crisis Solved’<br><a href="https://xkcd.com/3117/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">xkcd.com/3117/</span><span class="invisible"></span></a></p><p><a href="https://mastodon.social/tags/Science" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Science</span></a> <a href="https://mastodon.social/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <a href="https://mastodon.social/tags/XKCD" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>XKCD</span></a></p>
David Philip Morgan<p>Congratulations to <span class="h-card" translate="no"><a href="https://fediscience.org/@ElenLeFoll" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>ElenLeFoll</span></a></span> and colleagues on joining the German Reproducibility Network! 🎊 </p><p>Great to see representation of the humanities in <a href="https://mastodon.world/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> and <a href="https://mastodon.world/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a>, lots of great progress underway there - researchers <span class="h-card" translate="no"><a href="https://xn--baw-joa.social/@unimannheim" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>unimannheim</span></a></span> should definitely check out the talks from this initiative! 💡</p><p><span class="h-card" translate="no"><a href="https://mastodon.world/@GermanRepro" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>GermanRepro</span></a></span> <span class="h-card" translate="no"><a href="https://scicomm.xyz/@ReproducibiliTeaGlobal" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>ReproducibiliTeaGlobal</span></a></span> <span class="h-card" translate="no"><a href="https://fediscience.org/@ElenLeFoll" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>ElenLeFoll</span></a></span></p>
Pete Bachant<p>"One button" reproducibility should be the standard.</p><p><a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://fediscience.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a></p>
Daniel Hoffmann🌻<p>There is at least one subfield of biology where <a href="https://mathstodon.xyz/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> is relative high: fruit fly immunology where, according to a new study, the majority of results can be reproduced. I guess that a reason may be large sample sizes. <br><a href="https://www.nature.com/articles/d41586-025-02250-1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/d41586-025</span><span class="invisible">-02250-1</span></a></p>
petersuber<p>Retractions and failures to replicate are signs of weak research. But they're also signs of laudable and necessary efforts to identify weak research and improve future research. The <a href="https://fediscience.org/tags/Trump" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Trump</span></a> admin is systematically weaponizing these efforts to cast doubt on science as such. </p><p>"Research-integrity sleuths say their work is being ‘twisted’ to undermine science."<br><a href="https://www.nature.com/articles/d41586-025-02163-z" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/d41586-025</span><span class="invisible">-02163-z</span></a> </p><p><a href="https://fediscience.org/tags/DefendResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DefendResearch</span></a> <a href="https://fediscience.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <a href="https://fediscience.org/tags/Retractions" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Retractions</span></a> <a href="https://fediscience.org/tags/Trump" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Trump</span></a> <a href="https://fediscience.org/tags/TrumpVResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>TrumpVResearch</span></a> <a href="https://fediscience.org/tags/USPol" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>USPol</span></a> <a href="https://fediscience.org/tags/USPolitics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>USPolitics</span></a></p>
bladderbot<p><span class="h-card" translate="no"><a href="https://neuromatch.social/@elduvelle" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>elduvelle</span></a></span> Sure - let’s add to the problem of reproducibility (retraction rates are already much higher for high-impact journals, incl. Nature – Brembs et al 2013 "Deep impact: unintended consequences of journal rank." Frontiers in human Neuroscience) by adding AI peer reviewers and watch academic publishing enshittify further. <a href="https://mastodon.online/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> <a href="https://mastodon.online/tags/impactfactor" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>impactfactor</span></a> <a href="https://mastodon.online/tags/ScientificJournals" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ScientificJournals</span></a></p>
Dorothy Bishop<p>This bluesky thread by Mark Hanson describes a massive project to look at <a href="https://mastodon.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> of drosophila studies - I don't know much about that area, but the approach is pretty exciting and has potential for other topics. <a href="https://bsky.app/profile/hansonmark.bsky.social/post/3ltlvkkxyak2k" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bsky.app/profile/hansonmark.bs</span><span class="invisible">ky.social/post/3ltlvkkxyak2k</span></a></p>
Björn Brembs<p>The killer quote! Prestigious institutions and prestigious journals drive irreproducibility in the life sciences - well, at least in this particular sample.</p><p><a href="https://www.biorxiv.org/content/10.1101/2025.07.07.663460v2" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">25.07.07.663460v2</span></a></p><p><a href="https://mastodon.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> <a href="https://mastodon.social/tags/impactfactor" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>impactfactor</span></a></p>
Björn Brembs<p>And yet another one in the ever increasing list of analyses showing that top journals are bad for science:</p><p>"Thus, our analysis show major claims published in low-impact journals are significantly more likely to be reproducible than major claims published in trophy journals. "</p><p><a href="https://www.biorxiv.org/content/10.1101/2025.07.07.663460v2" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">25.07.07.663460v2</span></a></p><p><a href="https://mastodon.social/tags/publishing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>publishing</span></a> <a href="https://mastodon.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://mastodon.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a></p>
Björn Brembs<p>To my knowledge, first time that not only prestigious journals, but also prestigious institutions are implicated as major drivers of irreproducibility:</p><p>"Higher representation of challenged claims in trophy journals and from top universities"</p><p><a href="https://www.biorxiv.org/content/10.1101/2025.07.07.663460v2" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">25.07.07.663460v2</span></a></p><p><a href="https://mastodon.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> <a href="https://mastodon.social/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a></p>
EuroSciPy<p>🧑🔬 Starting your journey in scientific research?</p><p>Join the beginner-friendly tutorial at <a href="https://fosstodon.org/tags/EuroSciPy2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EuroSciPy2025</span></a>:<br>📦 Managing Scientific Data and Workflows with DataLad<br>Led by Ole Bialas &amp; Michał Szczepanik</p><p>In this hands-on session, you'll learn:<br>✅ How to organize &amp; track your data<br>✅ How to repeat your experiments reliably<br>✅ How to share your results with others</p><p>No Git experience required—just curiosity and Python basics!<br>📅 <a href="https://euroscipy.org/schedule" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">euroscipy.org/schedule</span><span class="invisible"></span></a><br><a href="https://fosstodon.org/tags/FAIRdata" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FAIRdata</span></a> <a href="https://fosstodon.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <a href="https://fosstodon.org/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Python</span></a></p>
Pete Bachant<p>Tips for using Jupyter notebooks as part of a reproducible workflow (one that goes from raw data to research article with a single command): <a href="https://docs.calkit.org/notebooks" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">docs.calkit.org/notebooks</span><span class="invisible"></span></a></p><p><a href="https://fediscience.org/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>openscience</span></a> <a href="https://fediscience.org/tags/jupyter" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>jupyter</span></a> <a href="https://fediscience.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a></p>
UniversityofGroningenLibrary<p>We invite staff and students at the University of <a href="https://social.edu.nl/tags/Groningen" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Groningen</span></a> to share how they are making <a href="https://social.edu.nl/tags/research" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>research</span></a> or <a href="https://social.edu.nl/tags/teaching" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>teaching</span></a> more open, accessible, transparent, or reproducible, for the 6th annual <a href="https://social.edu.nl/tags/OpenResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenResearch</span></a> Award. </p><p>Looking for inspiration?<br>Explore the case studies submitted in previous years:<br>🔗 <a href="https://www.rug.nl/research/openscience/open-research-award/previous-events" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">rug.nl/research/openscience/op</span><span class="invisible">en-research-award/previous-events</span></a></p><p>More info:<br>🔗 <a href="https://www.rug.nl/research/openscience/open-research-award/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">rug.nl/research/openscience/op</span><span class="invisible">en-research-award/</span></a></p><p><a href="https://social.edu.nl/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a> <a href="https://social.edu.nl/tags/OpenEducation" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenEducation</span></a> <a href="https://social.edu.nl/tags/OpenAccess" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenAccess</span></a> <a href="https://social.edu.nl/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Reproducibility</span></a> <br><span class="h-card" translate="no"><a href="https://mastodon.social/@oscgroningen" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>oscgroningen</span></a></span></p>
Elen Le Foll 🇫🇷 🇬🇧 🇩🇪<p>Jack Taylor is now presenting a new <a href="https://fediscience.org/tags/Rstats" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Rstats</span></a> package: "LexOPS: A Reproducible Solution to Stimuli Selection". Jack bravely did a live demonstration based on a German corpus ("because we're in Germany") that generated matched stimuli that certainly made the audience giggle... let's just say that one match involved the word "Erektion"... 😂 </p><p>There is a paper about the LexOPS package: <a href="https://link.springer.com/article/10.3758/s13428-020-01389-1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">link.springer.com/article/10.3</span><span class="invisible">758/s13428-020-01389-1</span></a> and a detailed tutorial: <a href="https://jackedtaylor.github.io/LexOPSdocs/index.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jackedtaylor.github.io/LexOPSd</span><span class="invisible">ocs/index.html</span></a>. Also a <a href="https://fediscience.org/tags/Shiny" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Shiny</span></a> app for those who really don't want to use R, but that allows code download for <a href="https://fediscience.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a>: <a href="https://jackedtaylor.github.io/LexOPSdocs/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jackedtaylor.github.io/LexOPSd</span><span class="invisible">ocs/</span></a> Really cool and useful project! <a href="https://fediscience.org/tags/WoReLa1" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>WoReLa1</span></a> <a href="https://fediscience.org/tags/linguistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>linguistics</span></a> <a href="https://fediscience.org/tags/psycholinguistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>psycholinguistics</span></a></p>
Dr Mircea Zloteanu ☀️ 🌊🌴<p><a href="https://mastodon.social/tags/statstab" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>statstab</span></a> #378 Selective Inference: The Silent Killer of Replicability</p><p>Thoughts: Benjamin overviews the replicability crisis, alternatives to p-values (and their issues), and suggests selective reporting is a large issue itself.</p><p><a href="https://mastodon.social/tags/replication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>replication</span></a> <a href="https://mastodon.social/tags/crisis" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>crisis</span></a> <a href="https://mastodon.social/tags/pvalue" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pvalue</span></a> <a href="https://mastodon.social/tags/nhst" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>nhst</span></a> <a href="https://mastodon.social/tags/selectivereporting" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>selectivereporting</span></a> <a href="https://mastodon.social/tags/replicability" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>replicability</span></a> <a href="https://mastodon.social/tags/reproducibility" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>reproducibility</span></a> </p><p><a href="https://hdsr.mitpress.mit.edu/pub/l39rpgyc/release/3" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">hdsr.mitpress.mit.edu/pub/l39r</span><span class="invisible">pgyc/release/3</span></a></p>