Livello Segreto

6 posts5 participants0 posts today

Luke PembletonAnyone have any experience using <a href="https://genomic.social/tags/AWS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AWS</a> workspaces or VNC as a <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> or <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> dev environment. I much prefer the idea of keeping dev on a local laptop and avoiding potential latency issues, keeping a single file system, and the ability to work on the go even without internet, but would be interested to hear others experiences.

devSJR :python: :rstats:Some time ago <a href="https://mastodon.social/@devTLB" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@devTLB</a> and I announced that we work on a review about <a href="https://fosstodon.org/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> packages for <a href="https://fosstodon.org/tags/bioimage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioimage</a> informatics. We think it is fairly complete now.We would be happy to get some feedback before we submit it.Here is the link to the draft:[Update: Copy on Codeberg] <a href="https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf</a><a href="https://fosstodon.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a>

Ivan Rossi :debian:[2504.06806] Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions<a href="https://arxiv.org/abs/2504.06806" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://arxiv.org/abs/2504.06806</a><a href="https://fosstodon.org/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AI</a> <a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Ivan Rossi :debian:[2504.03278] JanusDDG: A Thermodynamics-Compliant Model for Sequence-Based Protein Stability via Two-Fronts Multi-Head Attention<a href="https://arxiv.org/abs/2504.03278" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://arxiv.org/abs/2504.03278</a><a href="https://fosstodon.org/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AI</a> <a href="https://fosstodon.org/tags/llm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#llm</a> <a href="https://fosstodon.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

UK<a href="https://www.europesays.com/uk/10917/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.europesays.com/uk/10917/</a> Quantitative characterization of cell niches in spatially resolved omics data <a href="https://pubeurope.com/tags/Agriculture" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Agriculture</a> <a href="https://pubeurope.com/tags/AnimalGeneticsAndGenomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AnimalGeneticsAndGenomics</a> <a href="https://pubeurope.com/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://pubeurope.com/tags/Biomedicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Biomedicine</a> <a href="https://pubeurope.com/tags/CancerResearch" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CancerResearch</a> <a href="https://pubeurope.com/tags/DataMining" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DataMining</a> <a href="https://pubeurope.com/tags/GeneExpressionAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneExpressionAnalysis</a> <a href="https://pubeurope.com/tags/GeneFunction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GeneFunction</a> <a href="https://pubeurope.com/tags/general" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#general</a> <a href="https://pubeurope.com/tags/Genetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genetics</a> <a href="https://pubeurope.com/tags/HumanGenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HumanGenetics</a> <a href="https://pubeurope.com/tags/Science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Science</a> <a href="https://pubeurope.com/tags/software" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#software</a> <a href="https://pubeurope.com/tags/Transcriptomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Transcriptomics</a> <a href="https://pubeurope.com/tags/UK" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#UK</a> <a href="https://pubeurope.com/tags/UnitedKingdom" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#UnitedKingdom</a>

Bioinfhotep<a href="https://github.com/GabrielHoffman/GenomicDataStream" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/GabrielHoffman/GenomicDataStream</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/Rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Rstats</a> <a href="https://genomic.social/tags/GenomicsIO" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GenomicsIO</a> <a href="https://genomic.social/tags/StatGen" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StatGen</a>

bioinfhotep<a href="https://github.com/GabrielHoffman/GenomicDataStream" rel="nofollow noopener noreferrer" target="_blank">github.com/GabrielHoffm...</a> <a class="hashtag" href="https://bsky.app/search?q=%23Bioinformatics" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a class="hashtag" href="https://bsky.app/search?q=%23rstats" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a class="hashtag" href="https://bsky.app/search?q=%23GenomicsIO" rel="nofollow noopener noreferrer" target="_blank">#GenomicsIO</a> <a class="hashtag" href="https://bsky.app/search?q=%23StatGen" rel="nofollow noopener noreferrer" target="_blank">#StatGen</a> <a href="https://github.com/GabrielHoffman/GenomicDataStream" rel="nofollow noopener noreferrer" target="_blank">GitHub - GabrielHoffman/Genomi...</a>

Molecular Biology & EvolutionNew graph-based tool ska lo enables reference-free detection of SNPs, indels, and variant groups from pathogen WGS data. Benchmarking shows high sensitivity, including in regions with dense mutations.Link: <a href="https://doi.org/10.1093/molbev/msaf077" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1093/molbev/msaf077</a><a href="https://ecoevo.social/tags/NewPaperAlert" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NewPaperAlert</a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://ecoevo.social/tags/variantcalling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#variantcalling</a> <a href="https://ecoevo.social/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#genomics</a>

Boas PuckerExcited to share our latest preprint about CoExpPhylo: <a href="https://doi.org/10.1101/2025.04.03.647051" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1101/2025.04.03.647051</a>.Not long ago, Nele excelled at a <a href="https://mastodon.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> course for life scientists and acquired crucial skills for this work <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://mastodon.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DataScience</a> <a href="https://genomic.social/@PuckerLab" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@PuckerLab</a>

SIB Swiss Bioinformatics<a href="https://genomic.social/@bgeedb" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@bgeedb</a> was used to design stem-cell based vaccines 💉against <a href="https://mstdn.science/tags/cancer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cancer</a> in mouse models, opening a door to a potential application with humans.🔎 This is an example of the impact that <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> databases and tools developed by SIB groups have. Researchers use them to make sense of their data and tackle essential societal challenges.👉 Learn more: <a href="https://www.sib.swiss/services/open-software-and-databases/impact#designing-stem-cell-based-vaccines-against-cancer" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.sib.swiss/services/open-software-and-databases/impact#designing-stem-cell-based-vaccines-against-cancer</a><a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@marcrr</a> <a href="https://ecoevo.social/@fbastian" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@fbastian</a> <a href="https://mstdn.science/tags/SIBResourceImpacts" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SIBResourceImpacts</a> <a href="https://mstdn.science/tags/OpenSoftwareAndDatabases" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenSoftwareAndDatabases</a>

Moreno Colaiacovo 🧬🇮🇹Test your <a href="https://mastodon.uno/tags/coding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#coding</a> skills by solving these daily <a href="https://mastodon.uno/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> challenges 🧬biocode - Daily Programming Challenges <a href="https://www.biocodedaily.com/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biocodedaily.com/</a>

ivanfrOn Monday I received this email, sad news: <a href="https://mastodon.uno/tags/cipres" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cipres</a> <a href="https://mastodon.uno/tags/philogeny" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#philogeny</a> <a href="https://mastodon.uno/tags/biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biology</a> <a href="https://mastodon.uno/tags/bio" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bio</a> <a href="https://mastodon.uno/tags/genetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#genetic</a> <a href="https://mastodon.uno/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://mastodon.uno/tags/informatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#informatics</a> <a href="https://mastodon.uno/tags/taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#taxonomy</a> <a href="https://mastodon.uno/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.uno/tags/sci" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#sci</a> <a href="https://mastodon.uno/tags/philogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#philogenetics</a> <a href="https://mastodon.uno/tags/treeoflife" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#treeoflife</a> <a href="https://mastodon.uno/tags/CIPRES" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CIPRES</a> <a href="https://mastodon.uno/tags/populationgenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#populationgenetics</a> <a href="https://mastodon.uno/tags/code" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#code</a> <a href="https://mastodon.uno/tags/coding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#coding</a>

SIB Swiss Bioinformatics📣 The programme for the <a href="https://mstdn.science/tags/bc2basel" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bc2basel</a> tutorials & workshops is out! From <a href="https://mstdn.science/tags/geneexpression" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#geneexpression</a> analysis to <a href="https://mstdn.science/tags/machinelearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#machinelearning</a> or <a href="https://mstdn.science/tags/datavisualization" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#datavisualization</a>, beginner or advanced: boost your <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> skills!👉 Register to make sure to secure your spot (limited seats): <a href="https://tinyurl.com/3y8ay2d6" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://tinyurl.com/3y8ay2d6</a>

Christos Argyropoulos MD, PhDBless your heart <a href="https://mstdn.science/tags/Pubmed" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Pubmed</a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> <a href="https://academic.oup.com/bioinformatics/article/20/18/3363/202143?login=false" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://academic.oup.com/bioinformatics/article/20/18/3363/202143?login=false</a>

Thomas SandmannBig shoutout to the folks at NCBI GEO. They have been doing an incredible job managing enormous amounts of gene expression and related biomedical data for many, many years They do it efficiently and very, very well. I am so grateful: both when I download data published by others and when I submit my own data. You are true <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> heroes doing priceless and highly impactful work! 🦸 🧬 💻 <a href="https://genomic.social/tags/NCBI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NCBI</a> <a href="https://genomic.social/tags/nih" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nih</a>

Eli Roberson (he/him)<a href="https://genomic.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genomics</a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://genomic.social/tags/Academia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Academia</a>Beware US academic coders. If you have collaborators contributing code from a sanctioned region, your repos may be locked.See <a href="https://mastodon.social/@organicmaps/114155428924741370" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://mastodon.social/@organicmaps/114155428924741370</a>The kicker is that the US is leaning authoritarian and all in on censorship. If Canada or Mexico become sanction targets and you have code pushes from there, Microsoft will lock you out of your GitHub accounts.

Bioinfhotep<a href="https://link.springer.com/article/10.1186/s12859-025-06083-7" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://link.springer.com/article/10.1186/s12859-025-06083-7</a> <a href="https://genomic.social/tags/networksAnalysis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#networksAnalysis</a> <a href="https://genomic.social/tags/rstats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rstats</a> <a href="https://genomic.social/tags/methods" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#methods</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Egon Willigh☮gen 🟥I like to remind people, if you want less of my human rights, future, open science, and other opiniatied posts, follow my <a href="https://mastodon.social/tags/cheminformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cheminformatics</a> and <a href="https://mastodon.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> account at <a href="https://social.edu.nl/@egonw" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@egonw@social.edu.nl</a> Of course, I love you to stay here too, because I honestly believe in a better future and am hopeful. But hoping is not enough, hence my posts here.

Center for Health Data Science🐍Python II🐍Advance your <a href="https://datasci.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> skills in this 3-day <a href="https://datasci.social/tags/workshop" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#workshop</a> focusing on advanced <a href="https://datasci.social/tags/programming" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#programming</a> & <a href="https://datasci.social/tags/datascience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#datascience</a>.⚠ Requires Python I or equivalent experience.🗓 19–21 May 📍 Panum, University of Copenhagen ✏ Register: <a href="https://heads.ku.dk/calendar/2025/courses/python-2-spring-2025/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://heads.ku.dk/calendar/2025/courses/python-2-spring-2025/</a><a href="https://datasci.social/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a> <a href="https://datasci.social/tags/DataScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DataScience</a> <a href="https://datasci.social/tags/HeaDS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HeaDS</a> <a href="https://datasci.social/tags/UCPH" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#UCPH</a> <a href="https://datasci.social/tags/PhD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PhD</a> <a href="https://datasci.social/tags/HealthDataScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HealthDataScience</a> <a href="https://datasci.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://datasci.social/tags/MachineLearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MachineLearning</a> <a href="https://datasci.social/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AI</a> <a href="https://datasci.social/tags/BigData" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BigData</a> <a href="https://datasci.social/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://datasci.social/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RStats</a> <a href="https://datasci.social/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> <a href="https://datasci.social/tags/AcademicMastodon" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AcademicMastodon</a> <a href="https://datasci.social/tags/PrecisionMedicine" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PrecisionMedicine</a> <a href="https://datasci.social/tags/ComputationalBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ComputationalBiology</a> <a href="https://datasci.social/tags/Biostatistics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Biostatistics</a> <a href="https://datasci.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genomics</a>

naturepokerNext-next experiment might involve using adaptive sampling on the ONT platform. I'm curious, did anyone try adaptive sampling with older mid-GPU models, like 3060? Wondering if slower real-time basecalling on those cards will impact the output in someway. I'm thinking <a href="https://genomic.social/@Psy_Fer_" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@Psy_Fer_</a> might have the answer to this!<a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

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