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CSBJ💡 AI can predict protein structures — but can it predict how they behave?🔗 AlphaFold3 prediction of protein-protein complex: Is it ready for thermodynamic analysis?. Computational and Structural Biotechnology Journal, DOI: <a href="https://doi.org/10.1016/j.csbj.2025.10.015" rel="nofollow noopener" translate="no" target="_blank">https://doi.org/10.1016/j.csbj.2025.10.015</a>📚 CSBJ: <a href="https://www.csbj.org/" rel="nofollow noopener" translate="no" target="_blank">https://www.csbj.org/</a><a href="https://mastodon.social/tags/AlphaFold3" class="mention hashtag" rel="nofollow noopener" target="_blank">#AlphaFold3</a> <a href="https://mastodon.social/tags/ProteinDesign" class="mention hashtag" rel="nofollow noopener" target="_blank">#ProteinDesign</a> <a href="https://mastodon.social/tags/MolecularModeling" class="mention hashtag" rel="nofollow noopener" target="_blank">#MolecularModeling</a> <a href="https://mastodon.social/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> <a href="https://mastodon.social/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#StructuralBiology</a> <a href="https://mastodon.social/tags/Thermodynamics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Thermodynamics</a> <a href="https://mastodon.social/tags/ProteinProteinInteractions" class="mention hashtag" rel="nofollow noopener" target="_blank">#ProteinProteinInteractions</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

Christos Argyropoulos MD, PhDProfile HMMs and other Hidden Markov Models explained from we @weratedags.com at <a href="https://mstdn.science/tags/bsky" class="mention hashtag" rel="nofollow noopener" target="_blank">#bsky</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mstdn.science/tags/generativemodels" class="mention hashtag" rel="nofollow noopener" target="_blank">#generativemodels</a> <a href="https://mstdn.science/tags/probability" class="mention hashtag" rel="nofollow noopener" target="_blank">#probability</a> <a href="https://mstdn.science/tags/latentvariables" class="mention hashtag" rel="nofollow noopener" target="_blank">#latentvariables</a> <a href="https://mstdn.science/tags/statistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#statistics</a>

Christos Argyropoulos MD, PhD, FASN 🇺🇸 0kale/accProfile HMMs and other Hidden Markov Models explained from we <a class="mention h-card" href="https://bsky.app/profile/weratedags.com" rel="nofollow noopener" target="_blank">@weratedags.com</a> at <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23bsky" target="_blank">#bsky</a> <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23bioinformatics" target="_blank">#bioinformatics</a> <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23generativemodels" target="_blank">#generativemodels</a> <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23probability" target="_blank">#probability</a> <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23latentvariables" target="_blank">#latentvariables</a> <a class="hashtag" rel="nofollow noopener" href="https://bsky.app/search?q=%23statistics" target="_blank">#statistics</a>

Christos Argyropoulos MD PhDProfile HMMs and other Hidden Markov Models explained from we @weratedags.com at <a href="https://mastodon.social/tags/bsky" class="mention hashtag" rel="nofollow noopener" target="_blank">#bsky</a> <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.social/tags/generativemodels" class="mention hashtag" rel="nofollow noopener" target="_blank">#generativemodels</a> <a href="https://mastodon.social/tags/probability" class="mention hashtag" rel="nofollow noopener" target="_blank">#probability</a> <a href="https://mastodon.social/tags/latentvariables" class="mention hashtag" rel="nofollow noopener" target="_blank">#latentvariables</a> <a href="https://mastodon.social/tags/statistics" class="mention hashtag" rel="nofollow noopener" target="_blank">#statistics</a>

Dr. Robert M FlightI can be an idiot. 🤦‍♂️When trying to match chemicals by InChiKey across databases, it looks like I should be ignoring the last character, which is used to indicate charge (Neutral, Positive, Minus).Ugh. Well, that should help some of my analyses going forward.<a href="https://mastodon.social/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

Christian MeestersThis spring, we had a wonderful time at the CERN shaping the future of the Snakemake Workflow Management System during the Snakemake Hackathon. Next spring we will meet in Munich!If you want to take part in the Snakemake development, you can still register here: <a href="https://indico.cern.ch/e/snakemake-meeting-2026" rel="nofollow noopener" translate="no" target="_blank">https://indico.cern.ch/e/snakemake-meeting-2026</a><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#Snakemake</a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#HPC</a> <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://fediscience.org/tags/physics" class="mention hashtag" rel="nofollow noopener" target="_blank">#physics</a> <a href="https://fediscience.org/tags/dataanalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#dataanalysis</a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener" target="_blank">#ReproducibleComputing</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a>

nf-corePipeline release! nf-core/bacass v2.5.0 - nf-core/bacass v2.5.0!Please see the changelog: <a href="https://github.com/nf-core/bacass/releases/tag/2.5.0" rel="nofollow noopener" translate="no" target="_blank">https://github.com/nf-core/bacass/releases/tag/2.5.0</a><a href="https://mstdn.science/tags/assembly" class="mention hashtag" rel="nofollow noopener" target="_blank">#assembly</a> <a href="https://mstdn.science/tags/bacterialgenomes" class="mention hashtag" rel="nofollow noopener" target="_blank">#bacterialgenomes</a> <a href="https://mstdn.science/tags/denovo" class="mention hashtag" rel="nofollow noopener" target="_blank">#denovo</a> <a href="https://mstdn.science/tags/denovoassembly" class="mention hashtag" rel="nofollow noopener" target="_blank">#denovoassembly</a> <a href="https://mstdn.science/tags/genomeassembly" class="mention hashtag" rel="nofollow noopener" target="_blank">#genomeassembly</a> <a href="https://mstdn.science/tags/hybridassembly" class="mention hashtag" rel="nofollow noopener" target="_blank">#hybridassembly</a> <a href="https://mstdn.science/tags/nanopore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nanopore</a> <a href="https://mstdn.science/tags/nanoporesequencing" class="mention hashtag" rel="nofollow noopener" target="_blank">#nanoporesequencing</a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener" target="_blank">#openscience</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener" target="_blank">#nextflow</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

jobRxivPostdoc: Metagenomics of Oil Field Samples University of Calgary Join of an interdisciplinary research team (>20 people) that uses metagenomics and molecular biology to analyze environmental and industrial samplesSee the full job description on jobRxiv: <a href="https://jobrxiv.org/job/university-of-calgary-27778-postdoc-metagenomics-of-oil-field-samples/" rel="nofollow noopener" translate="no" target="_blank">https://jobrxiv.org/job/university-of-calgary-27778-postdoc-metagenomics-of-oil-field-samples/</a><a href="https://mas.to/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mas.to/tags/environmentalmicro" class="mention hashtag" rel="nofollow noopener" target="_blank">#environmentalmicro</a>... <a href="https://jobrxiv.org/job/university-of-calgary-27778-postdoc-metagenomics-of-oil-field-samples/?fsp_sid=4085" rel="nofollow noopener" translate="no" target="_blank">https://jobrxiv.org/job/university-of-calgary-27778-postdoc-metagenomics-of-oil-field-samples/?fsp_sid=4085</a>

galaxyprojectThe Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025. <a href="https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/" rel="nofollow noopener" translate="no" target="_blank">https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/</a><a href="https://xn--baw-joa.social/@galaxyfreiburg" class="u-url mention" rel="nofollow noopener" target="_blank">@galaxyfreiburg</a> <a href="https://mstdn.science/tags/UseGalaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#UseGalaxy</a> <a href="https://mstdn.science/tags/GalaxyProject" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyProject</a> <a href="https://mstdn.science/tags/EOSC" class="mention hashtag" rel="nofollow noopener" target="_blank">#EOSC</a> <a href="https://mstdn.science/tags/SingleCell" class="mention hashtag" rel="nofollow noopener" target="_blank">#SingleCell</a> <a href="https://mstdn.science/tags/SpatialOmics" class="mention hashtag" rel="nofollow noopener" target="_blank">#SpatialOmics</a> <a href="https://mstdn.science/tags/Omics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Omics</a> <a href="https://mstdn.science/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Transcriptomics</a> <a href="https://mstdn.science/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://mstdn.science/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genomics</a> <a href="https://mstdn.science/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#ComputationalBiology</a> <a href="https://mstdn.science/tags/EuroScienceGateway" class="mention hashtag" rel="nofollow noopener" target="_blank">#EuroScienceGateway</a> <a href="https://mstdn.science/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://mstdn.science/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#ReproducibleResearch</a> <a href="https://mstdn.science/tags/GalaxyCommunity" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyCommunity</a> <a href="https://mstdn.science/tags/SPOC" class="mention hashtag" rel="nofollow noopener" target="_blank">#SPOC</a> (1/2)

Dr. Robert M FlightChemical representation standardization needed to generalize metabolic pathway involvement prediction across the Kyoto Encyclopedia of Genes and Genomes, Reactome, and MetaCyc knowledgebases<a href="https://www.biorxiv.org/content/10.1101/2025.04.02.646918v1" rel="nofollow noopener" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2025.04.02.646918v1</a><a href="https://mastodon.social/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://mastodon.social/tags/UsefulMachineLearning" class="mention hashtag" rel="nofollow noopener" target="_blank">#UsefulMachineLearning</a>

Dr. Robert M FlightRE: <a href="https://mastodon.social/@rmflight/115380117804495322" rel="nofollow noopener" translate="no" target="_blank">https://mastodon.social/@rmflight/115380117804495322</a>Related to this, another member of our research group has been working on predicting which pathways a given compound is likely associated with, just based on structure alone, learning from all of the current data available (see next post).Thankfully, I was able to generate mol files for all of my compounds, and they were able to put them through the prediction pipeline! Which should include all the original pathways they are in, as well as actual predictions.<a href="https://mastodon.social/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

Dave TabbI am replacing the Microsoft <a href="https://mastodon.africa/tags/Excel" class="mention hashtag" rel="nofollow noopener" target="_blank">#Excel</a> figures in my PowerPoint with <a href="https://mastodon.africa/tags/ggplot" class="mention hashtag" rel="nofollow noopener" target="_blank">#ggplot</a> figures to avoid public humiliation? Yes, Yes I am. <a href="https://mastodon.africa/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a>

Galaxy-Team der Uni FreiburgGalaxy can be adjusted for sensitive data. In the Netherlands, a GDPR-compliant Galaxy clone runs in an isolated network, converting Toolshed tools to Apptainer containers—secure, auditable, and reproducible. Read more: <a href="https://galaxyproject.org/news/2025-01-20-esg-w-p5/" rel="nofollow noopener" translate="no" target="_blank">https://galaxyproject.org/news/2025-01-20-esg-w-p5/</a><a href="https://xn--baw-joa.social/tags/UseGalaxy" class="mention hashtag" rel="nofollow noopener" target="_blank">#UseGalaxy</a> <a href="https://xn--baw-joa.social/tags/GalaxyProject" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyProject</a> <a href="https://xn--baw-joa.social/tags/UniFreiburg" class="mention hashtag" rel="nofollow noopener" target="_blank">#UniFreiburg</a> <a href="https://xn--baw-joa.social/tags/EOSC" class="mention hashtag" rel="nofollow noopener" target="_blank">#EOSC</a> <a href="https://xn--baw-joa.social/tags/EuroScienceGateway" class="mention hashtag" rel="nofollow noopener" target="_blank">#EuroScienceGateway</a> <a href="https://xn--baw-joa.social/tags/SensitiveData" class="mention hashtag" rel="nofollow noopener" target="_blank">#SensitiveData</a> <a href="https://xn--baw-joa.social/tags/GDPR" class="mention hashtag" rel="nofollow noopener" target="_blank">#GDPR</a> <a href="https://xn--baw-joa.social/tags/PrivacyByDesign" class="mention hashtag" rel="nofollow noopener" target="_blank">#PrivacyByDesign</a> <a href="https://xn--baw-joa.social/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#ReproducibleResearch</a> <a href="https://xn--baw-joa.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://xn--baw-joa.social/tags/Apptainer" class="mention hashtag" rel="nofollow noopener" target="_blank">#Apptainer</a> <a href="https://xn--baw-joa.social/tags/DataGovernance" class="mention hashtag" rel="nofollow noopener" target="_blank">#DataGovernance</a> <a href="https://xn--baw-joa.social/tags/Netherlands" class="mention hashtag" rel="nofollow noopener" target="_blank">#Netherlands</a>

Jorge Guerra Pires, Ph.D.Dear all, I am glad to announce that the final version of my paper is now available. One interesting fact: you can see all the reviewers’ comments and my replies. I believe this transparency is important for understanding why and how the paper was accepted. I fully support this new system of openness.<a href="https://mastodon.social/tags/medicine" class="mention hashtag" rel="nofollow noopener" target="_blank">#medicine</a> <a href="https://mastodon.social/tags/chatbots" class="mention hashtag" rel="nofollow noopener" target="_blank">#chatbots</a> <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> <a href="https://mastodon.social/tags/chatGPT" class="mention hashtag" rel="nofollow noopener" target="_blank">#chatGPT</a> <a href="https://mastodon.social/tags/LLM" class="mention hashtag" rel="nofollow noopener" target="_blank">#LLM</a> <a href="https://mastodon.social/tags/artificialintelligence" class="mention hashtag" rel="nofollow noopener" target="_blank">#artificialintelligence</a> <a href="https://xmed.jmir.org/2025/1/e56090" rel="nofollow noopener" translate="no" target="_blank">https://xmed.jmir.org/2025/1/e56090</a>

nf-core🧑🏾‍💻 Need help with anything <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener" target="_blank">#nfcore</a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener" target="_blank">#nextflow</a> ( <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> ) <a href="https://mstdn.science/tags/pipelines" class="mention hashtag" rel="nofollow noopener" target="_blank">#pipelines</a>, whether running or developing? ⏰ Today's EMEA friendly weekly helpdesk is at 10:00 CEST (Berlin time) (please see <a href="https://mstdn.science/tags/weekly" class="mention hashtag" rel="nofollow noopener" target="_blank">#weekly</a>-helpdesk on the nf-core Slack for connection details!)📅 Note that we also have other regular helpdesks for different TZs!- 🌏 Asia-Pacific: Wednesdays @ 15:00 NZDT - 🌎 Americas: Tuesdays @ 14:00 ETJoin the nf-core slack for more details and reminders!

Dr. Robert M FlightSome days, I really, really dislike my job.Saliva metabolomics project, with a new core doing the metabolomics that I've never worked with their data.InChiKey seems to be the most reliable thing to work with, given I've gotten all the CheBI InChiKey's generated from their InChi strings (thanks OpenBabel!). And Reactome pathways has a mapping to CheBI, so great!But, but, the InChiKey given from core for Riboflavin, doesn't get me to the Reactome pathway!<a href="https://mastodon.social/tags/Metabolomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Metabolomics</a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>

naturepokerAlright, <a href="https://genomic.social/tags/guix" class="mention hashtag" rel="nofollow noopener" target="_blank">#guix</a> package manager, <a href="https://genomic.social/tags/emacs" class="mention hashtag" rel="nofollow noopener" target="_blank">#emacs</a> and <a href="https://genomic.social/tags/guile" class="mention hashtag" rel="nofollow noopener" target="_blank">#guile</a> running in replicable manner across three different machines, two different types of distros. As long as you don't have to deal with selinux it's pretty trouble free. Very much an improved experience from when I first tried it a couple of years ago. I should do a quick write up later today. Next step, figuring out guix shell&home, testing <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#bioinformatics</a> stuff.

galaxyprojectNew workflow from the Galaxy Community! A reproducible workflow for microbial gene analysis (open, FAIR, and ready to explore). Explore the power of Galaxy for microbiome and genomics research: <a href="https://galaxyproject.org/news/2025-09-26-microbial-gene-workflow/" rel="nofollow noopener" translate="no" target="_blank">https://galaxyproject.org/news/2025-09-26-microbial-gene-workflow/</a><a href="https://xn--baw-joa.social/@galaxyfreiburg" class="u-url mention" rel="nofollow noopener" target="_blank">@galaxyfreiburg</a> <a href="https://mstdn.science/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://mstdn.science/tags/GenomeAnalysis" class="mention hashtag" rel="nofollow noopener" target="_blank">#GenomeAnalysis</a> <a href="https://mstdn.science/tags/MicrobialGenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#MicrobialGenomics</a> <a href="https://mstdn.science/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenScience</a> <a href="https://mstdn.science/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#ReproducibleResearch</a> <a href="https://mstdn.science/tags/GalaxyProject" class="mention hashtag" rel="nofollow noopener" target="_blank">#GalaxyProject</a> <a href="https://mstdn.science/tags/OpenSourceTools" class="mention hashtag" rel="nofollow noopener" target="_blank">#OpenSourceTools</a> <a href="https://mstdn.science/tags/LifeSciences" class="mention hashtag" rel="nofollow noopener" target="_blank">#LifeSciences</a> <a href="https://mstdn.science/tags/ResearchTools" class="mention hashtag" rel="nofollow noopener" target="_blank">#ResearchTools</a>

Melbourne BioinformaticsWhether your background is in biology, biomedicine, mathematics/statistics, or computer science, there’s an entry point for you into the University of Melbourne's Master of Science (<a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a>). Apply now for the March 2026 intake! <a href="https://mdhs.unimelb.edu.au/melbournebioinformatics/teaching/master-of-science-bioinformatics" rel="nofollow noopener" translate="no" target="_blank">https://mdhs.unimelb.edu.au/melbournebioinformatics/teaching/master-of-science-bioinformatics</a>

Boas PuckerRE: <a href="https://mastodon.social/@boas_pucker/115370863020490974" rel="nofollow noopener" translate="no" target="_blank">https://mastodon.social/@boas_pucker/115370863020490974</a>What is your favourite gene duplication example? We would love to include some additional cases for benchmarking. Please comment below. <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Bioinformatics</a> <a href="https://mastodon.social/tags/Python" class="mention hashtag" rel="nofollow noopener" target="_blank">#Python</a> <a href="https://mastodon.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#Genomics</a> <a href="https://mastodon.social/tags/Evolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#Evolution</a>

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