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#bioinformatics

16 posts11 participants0 posts today
Dr. Robert M Flight<p>Saw a Reddit post about a "Peer Review LLM", and I decided to test it with one of my own current preprints to see how good it actually is. </p><p>As I expected, it's rubbish, at least in the context of what one should actually expect from a peer review, because an LLM doesn't actually *think*.</p><p>You can see it's output here:</p><p><a href="https://bgpt.pro/?q=Paper%20Review%3A%20Information-Content-Informed%20Kendall-tau%20Correlation%20Methodology%3A%20Interpreting%20Missing%20Values%20as%20Useful%20Information" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bgpt.pro/?q=Paper%20Review%3A%</span><span class="invisible">20Information-Content-Informed%20Kendall-tau%20Correlation%20Methodology%3A%20Interpreting%20Missing%20Values%20as%20Useful%20Information</span></a></p><p>/1</p><p><a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mastodon.social/tags/LLM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>LLM</span></a> <a href="https://mastodon.social/tags/academia" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>academia</span></a> <a href="https://mastodon.social/tags/PublishOrPerish" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PublishOrPerish</span></a></p>
Ben Cardoen<p>Bioinformatics.ca has regular workshops on bioinformatics (R/Python/omics), now also open to non Canadian residents<br><a href="https://bioinformatics.ca/workshops-all/2025-pathogen-genomic-epidemiology-online/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">bioinformatics.ca/workshops-al</span><span class="invisible">l/2025-pathogen-genomic-epidemiology-online/</span></a><br><a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Dave Lunt<p>I’m currently trying to workflow together all my DNA sequence cleaning and munging as although each issue is rare there’s ALWAYS some problem. The goal is automatically creating clean and well behaved sequence data. Though there may always be a novel problem waiting to say hello! <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a></p>
naturepoker<p>Minimod preprint from <span class="h-card" translate="no"><a href="https://genomic.social/@hasindu2008" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>hasindu2008</span></a></span> gang is out. Code available <a href="https://github.com/warp9seq/minimod" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">github.com/warp9seq/minimod</span><span class="invisible"></span></a></p><p>I love the work they're doing with slow5/blow5 open spec for ONT raw data, and archive all internal reads using them. Really need to sit down and test this one out with my <a href="https://genomic.social/tags/archaea" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>archaea</span></a> raw data!</p><p><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/methylation" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>methylation</span></a> <a href="https://genomic.social/tags/ONT" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ONT</span></a> <a href="https://genomic.social/tags/sequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>sequencing</span></a></p>
J of Systematics and Evolution<p>A feast for *all* the senses!<br>Dr. Douglas Chesters addresses the gap in public information on <a href="https://mstdn.science/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>phylogenetics</span></a> for nonvisual modalities with a <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> pipeline to represent phylogenies in <a href="https://mstdn.science/tags/audio" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>audio</span></a> and <a href="https://mstdn.science/tags/video" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>video</span></a> forms!<br><a href="https://doi.org/10.1111/jse.13195" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">doi.org/10.1111/jse.13195</span><span class="invisible"></span></a> <br>@WileyEcolEvol<br> <a href="https://mstdn.science/tags/JSE" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>JSE</span></a> <a href="https://mstdn.science/tags/SciComm" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SciComm</span></a></p>
Bose-Einstein-Kondensat<p><a href="https://mstdn.social/tags/MolPrint3D" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolPrint3D</span></a>: A <a href="https://mstdn.social/tags/Blender" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Blender</span></a> add-on for enhanced <a href="https://mstdn.social/tags/3Dprinting" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>3Dprinting</span></a> of ball-and-stick <a href="https://mstdn.social/tags/molecular" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>molecular</span></a> models:<br><a href="https://doi.org/10.1021/acs.jchemed.7b00549" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1021/acs.jchemed.7b</span><span class="invisible">00549</span></a><br><a href="https://mstdn.social/tags/DIYbio" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>DIYbio</span></a> <a href="https://mstdn.social/tags/chemistry" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>chemistry</span></a> <a href="https://mstdn.social/tags/lab" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>lab</span></a> <a href="https://mstdn.social/tags/CompChem" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>CompChem</span></a> <a href="https://mstdn.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mstdn.social/tags/visualization" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>visualization</span></a> <a href="https://mstdn.social/tags/MINT" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MINT</span></a> <a href="https://mstdn.social/tags/STEM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>STEM</span></a> <a href="https://mstdn.social/tags/EDU" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EDU</span></a> <a href="https://mstdn.social/tags/school" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>school</span></a> <a href="https://mstdn.social/tags/Schule" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Schule</span></a> <a href="https://mstdn.social/tags/education" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>education</span></a></p>
Luke Pembleton<p>On NCBI what determines which genome assembly gets the green 'reference" star tag? I'm seeming a scaffold level assembly with 40X coverage from 2019 getting the 'reference' star whilst a complete chromosome scale assembly with 300X coverage from 2021 for the same species not... Is this a community driven label that just takes time to update?<br><a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Peter Cock<p>I do like the <a href="https://fediscience.org/tags/AlcareersISMB25" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AlcareersISMB25</span></a> panel setup at the <a href="https://fediscience.org/tags/ISMBECCB2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ISMBECCB2025</span></a> UK <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> track - the projector has a minimal biography for each panellist (left to right in same order)</p>
Peter Cock<p><a href="https://fediscience.org/tags/ISMBECCB2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ISMBECCB2025</span></a> flyer during the UK <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> track for their panel session:</p><p>CAREERS AND TRAJECTORIES IN AI<br>Help shape the discussion!</p><p>1️⃣Scan QR code or visit Slido.com 4078238<br>2️⃣ Read questions and upvote/downvote preference<br>3️⃣ Submit a new question for the panel if not above<br>4️⃣ Top voted questions will be answered first</p><p>Thoughts on the event? Tag us: <a href="https://fediscience.org/tags/AlcareersISMB25" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>AlcareersISMB25</span></a></p>
jobRxiv<p>PostDoctoral Position in Bioinformatics </p><p>Universidade Estadual de Campinas</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/universidade-estadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97738" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/universidade-e</span><span class="invisible">stadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97738</span></a></p><p><a href="https://mas.to/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mas.to/tags/ScienceJobs" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ScienceJobs</span></a> <a href="https://mas.to/tags/hiring" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>hiring</span></a> <a href="https://mas.to/tags/research" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>research</span></a><br><a href="https://jobrxiv.org/job/universidade-estadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97738" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/universidade-e</span><span class="invisible">stadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97738</span></a></p>
Peter Cock<p><span class="h-card" translate="no"><a href="https://genomic.social/@OpenBio" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>OpenBio</span></a></span> Wow - Nigeria has close to 20% of Africa's population? That means a lot of young educated people, and indirectly high demand for <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> training...</p>
Open Bioinformatics Foundation<p>Successful first remote talk, but switching to plan B and a pre-recorded video from the other remote speaker at <a href="https://genomic.social/tags/BOSC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BOSC2025</span></a>:</p><p>Seun Olufemi "Connecting Data, People, and Purpose: How Open Science is Advancing <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> in a Low-Resource region (<a href="https://genomic.social/tags/Nigeria" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Nigeria</span></a>)"</p>
Peter Cock<p>Based on the show of hands just now, half the <a href="https://fediscience.org/tags/BOSC2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BOSC2025</span></a> attendees are at their first BOSC (<a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://fediscience.org/tags/OpenSource" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenSource</span></a> Conference) 🎉</p>
Johannes Köster<p><a href="https://fosstodon.org/tags/vembrane" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>vembrane</span></a>, our CLI tool for manipulating VCF/BCF files via Python expressions has gained a new subcommand for sorting. Use it to sort by impact, pathogenicity, frequencies, or any complex Python logic, e.g. for variant prioritization.<br><a href="https://github.com/vembrane/vembrane/blob/main/docs/sort.md" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/vembrane/vembrane/b</span><span class="invisible">lob/main/docs/sort.md</span></a><br><a href="https://fosstodon.org/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Marc Robinson-Rechavi<p>I think we're going to get a lot of discussions of <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> resources funding and sustainability during <a href="https://ecoevo.social/tags/ismbeccb2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ismbeccb2025</span></a></p>
Marc Robinson-Rechavi<p>Good point of <span class="h-card" translate="no"><a href="https://mastodon.social/@bffo" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>bffo</span></a></span> that licensing to companies limits re-usability of resources, contra <a href="https://ecoevo.social/tags/FAIR" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>FAIR</span></a> principles. Yet we need to find a sustainable model for our <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://ecoevo.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>biocuration</span></a> resources. <a href="https://ecoevo.social/tags/ismbeccb2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ismbeccb2025</span></a></p>
Marc Robinson-Rechavi<p>Great choice of ISCB 2025 Accomplishments by a Senior Scientist: Amos Bairoch, 45 years of <a href="https://ecoevo.social/tags/biocuration" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>biocuration</span></a> which are foundational to our knowledge of biology in <a href="https://ecoevo.social/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ComputationalBiology</span></a> <a href="https://ecoevo.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a>. <a href="https://ecoevo.social/tags/ismbeccb2025" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ismbeccb2025</span></a> <span class="h-card" translate="no"><a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>SIB</span></a></span></p>
Europe Says<p><a href="https://www.europesays.com/2259441/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">europesays.com/2259441/</span><span class="invisible"></span></a> SCNT: an R package for data analysis and visualization of single-cell and spatial transcriptomics | BMC Bioinformatics #<a href="https://pubeurope.com/tags/%C3%A1r" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ár</span></a> <a href="https://pubeurope.com/tags/algorithms" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>algorithms</span></a> <a href="https://pubeurope.com/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioinformatics</span></a> <a href="https://pubeurope.com/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ComputationalBiology</span></a>/Bioinformatics <a href="https://pubeurope.com/tags/ComputerAppl" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ComputerAppl</span></a>.InLifeSciences <a href="https://pubeurope.com/tags/Data" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Data</span></a> <a href="https://pubeurope.com/tags/ggplot2" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ggplot2</span></a> <a href="https://pubeurope.com/tags/Microarrays" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Microarrays</span></a> <a href="https://pubeurope.com/tags/SCNT" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SCNT</span></a> <a href="https://pubeurope.com/tags/SingleCellSequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SingleCellSequencing</span></a> <a href="https://pubeurope.com/tags/SpatialTranscriptomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SpatialTranscriptomics</span></a></p>
Pierre Lindenbaum<p>🇫🇷 ça recrute chez moi: <a href="https://umr1087.univ-nantes.fr/job-vacancies-internships/job/ingenieur-e-biologiste-en-traitement-de-donnees-bio-informaticien-ne" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">umr1087.univ-nantes.fr/job-vac</span><span class="invisible">ancies-internships/job/ingenieur-e-biologiste-en-traitement-de-donnees-bio-informaticien-ne</span></a></p><p>"Ingénieur.e biologiste en traitement de données – Bio-informaticien.ne"</p><p><a href="https://genomic.social/tags/France" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>France</span></a> <a href="https://genomic.social/tags/bioinformatique" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatique</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/nantes" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>nantes</span></a> <a href="https://genomic.social/tags/job" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>job</span></a> <a href="https://genomic.social/tags/emploi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>emploi</span></a></p>
jobRxiv<p>PostDoctoral Position in Bioinformatics </p><p>Universidade Estadual de Campinas</p><p>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/universidade-estadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97598" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/universidade-e</span><span class="invisible">stadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97598</span></a></p><p><a href="https://mas.to/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://mas.to/tags/ScienceJobs" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ScienceJobs</span></a> <a href="https://mas.to/tags/hiring" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>hiring</span></a> <a href="https://mas.to/tags/research" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>research</span></a><br><a href="https://jobrxiv.org/job/universidade-estadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97598" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">jobrxiv.org/job/universidade-e</span><span class="invisible">stadual-de-campinas-27778-postdoctoral-position-in-bioinformatics/?feed_id=97598</span></a></p>