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#bioinformatics

35 posts32 participants3 posts today
Luke Pembleton<p>Cloud computing: where you're not just a bioinformatician, you’re also the finance manager, compliance officer, and IT support, all while carrying a hefty dose of mental fatigue. I miss those PhD days with a inhouse HPC when all you had to do was sbatch every parameter combo under the sun to test your research question… then complain about queue times and who was clogging the damn cluster with their BLAST jobs 😅<br><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Luke Pembleton<p>The joys of windows line endings creeping into your Linux workflows... <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
SIB Swiss Bioinformatics<p><span class="h-card" translate="no"><a href="https://genomic.social/@bgeedb" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>bgeedb</span></a></span> 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">#<span>cancer</span></a> in mouse models, opening a door to a potential application with humans.</p><p>🔎 This is an example of the impact that <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> databases and tools developed by SIB groups have. Researchers use them to make sense of their data and tackle essential societal challenges.</p><p>👉 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"><span class="invisible">https://www.</span><span class="ellipsis">sib.swiss/services/open-softwa</span><span class="invisible">re-and-databases/impact#designing-stem-cell-based-vaccines-against-cancer</span></a></p><p><span class="h-card" translate="no"><a href="https://ecoevo.social/@marcrr" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>marcrr</span></a></span> <span class="h-card" translate="no"><a href="https://ecoevo.social/@fbastian" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>fbastian</span></a></span> </p><p><a href="https://mstdn.science/tags/SIBResourceImpacts" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SIBResourceImpacts</span></a> <a href="https://mstdn.science/tags/OpenSoftwareAndDatabases" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenSoftwareAndDatabases</span></a></p>
Moreno Colaiacovo 🧬🇮🇹<p>Test your <a href="https://mastodon.uno/tags/coding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>coding</span></a> skills by solving these daily <a href="https://mastodon.uno/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> challenges 🧬</p><p>biocode - Daily Programming Challenges<br><a href="https://www.biocodedaily.com/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="">biocodedaily.com/</span><span class="invisible"></span></a></p>
Benjamin Carr, Ph.D. 👨🏻‍💻🧬<p><a href="https://hachyderm.io/tags/Genetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Genetic</span></a> data repo <a href="https://hachyderm.io/tags/OpenSNP" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenSNP</span></a> to self-destruct before authoritarians weaponize it<br>The reason, according to <a href="https://hachyderm.io/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> researcher Bastian Greshake Tzovaras, one of the founders of the project, is the dissolution of genetic testing biz <a href="https://hachyderm.io/tags/23andMe" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>23andMe</span></a> and the potential weaponization of genetic data by <a href="https://hachyderm.io/tags/farright" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>farright</span></a> <a href="https://hachyderm.io/tags/authoritarian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>authoritarian</span></a> regimes. <br><a href="https://www.theregister.com/2025/04/01/opensnp_shutdown/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">theregister.com/2025/04/01/ope</span><span class="invisible">nsnp_shutdown/</span></a></p>
ivanfr<p>On Monday I received this email, sad news: <br><a href="https://mastodon.uno/tags/cipres" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>cipres</span></a> <a href="https://mastodon.uno/tags/philogeny" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>philogeny</span></a> <a href="https://mastodon.uno/tags/biology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>biology</span></a> <a href="https://mastodon.uno/tags/bio" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bio</span></a> <a href="https://mastodon.uno/tags/genetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>genetic</span></a> <a href="https://mastodon.uno/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> <a href="https://mastodon.uno/tags/informatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>informatics</span></a> <a href="https://mastodon.uno/tags/taxonomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>taxonomy</span></a> <a href="https://mastodon.uno/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>science</span></a> <a href="https://mastodon.uno/tags/sci" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>sci</span></a> <a href="https://mastodon.uno/tags/philogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>philogenetics</span></a> <a href="https://mastodon.uno/tags/treeoflife" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>treeoflife</span></a> <a href="https://mastodon.uno/tags/CIPRES" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CIPRES</span></a> <a href="https://mastodon.uno/tags/populationgenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>populationgenetics</span></a> <a href="https://mastodon.uno/tags/code" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>code</span></a> <a href="https://mastodon.uno/tags/coding" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>coding</span></a></p>
Mark Ziemann 🇺🇦<p>The mitch R/Bioconductor package for enrichment analysis gets new network visualisation function in the devel branch. See these examples for how lung cells respond to C19 infection. Here red=up regulated, blue=down.<br>Details and quickstart guide: <a href="https://genomespot.blogspot.com/2025/04/mitch-gets-upgraded-now-with-gene-set.html" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">genomespot.blogspot.com/2025/0</span><span class="invisible">4/mitch-gets-upgraded-now-with-gene-set.html</span></a><br><a href="https://genomic.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Genomics</span></a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>dataviz</span></a></p>
naturepoker<p>I'm thinking of submitting an Archaeal RNAseq project here.</p><p>Anyone around here in touch with someone at Ultima Genomics? Their sequencing submission web form might have a permission issue :/ </p><p><a href="https://www.ultimagenomics.com/count-on-us/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">ultimagenomics.com/count-on-us</span><span class="invisible">/</span></a></p><p><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Pierre Lindenbaum<p>asking for a friend: do you know any database/framework to visualize RNAseq data ? (just like <a href="https://github.com/broadinstitute/gnomad-browser" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/broadinstitute/gnom</span><span class="invisible">ad-browser</span></a> for WGS)</p><p><a href="https://genomic.social/tags/database" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>database</span></a> <a href="https://genomic.social/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>rnaseq</span></a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Guillaume Louvel<p>I'm writing way to much <a href="https://ecoevo.social/tags/awk" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>awk</span></a> code than I should...</p><p><a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
nf-core<p>Pipeline release! nf-core/variantbenchmarking v1.2.0 - 1.2.0 Doubtful Adams!</p><p>Please see the changelog: <a href="https://github.com/nf-core/variantbenchmarking/releases/tag/1.2.0" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/nf-core/variantbenc</span><span class="invisible">hmarking/releases/tag/1.2.0</span></a></p><p><a href="https://mstdn.science/tags/benchmark" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>benchmark</span></a> <a href="https://mstdn.science/tags/draft" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>draft</span></a> <a href="https://mstdn.science/tags/structuralvariants" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>structuralvariants</span></a> <a href="https://mstdn.science/tags/variantcalling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>variantcalling</span></a> <a href="https://mstdn.science/tags/nfcore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nfcore</span></a> <a href="https://mstdn.science/tags/openscience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>openscience</span></a> <a href="https://mstdn.science/tags/nextflow" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>nextflow</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
Bioconductor<p>🎉 Announcing the EuroBioC2025 Sticker Design Winner! 🎉</p><p>🏆 Winner: Chaima Hkimi</p><p>🎨 Chaima’s design draws on some of Barcelona’s most iconic landmarks, featuring the Sagrada Família and the vibrant colours of Park Güell. She even swapped the 'i' in 'BioC' for the Bioconductor logo — a creative nod to the project!</p><p>Thanks to everyone who submitted a design. You’ll be able to pick up Chaima’s sticker at EuroBioC2025!</p><p><a href="https://genomic.social/tags/EuroBioC2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>EuroBioC2025</span></a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioconductor</span></a> <a href="https://genomic.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://genomic.social/tags/RStats" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RStats</span></a> <a href="https://genomic.social/tags/StickerContest" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>StickerContest</span></a></p>
SIB Swiss Bioinformatics<p>📣 The programme for the <a href="https://mstdn.science/tags/bc2basel" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bc2basel</span></a> tutorials &amp; workshops is out! From <a href="https://mstdn.science/tags/geneexpression" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>geneexpression</span></a> analysis to <a href="https://mstdn.science/tags/machinelearning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>machinelearning</span></a> or <a href="https://mstdn.science/tags/datavisualization" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>datavisualization</span></a>, beginner or advanced: boost your <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> skills!</p><p>👉 Register to make sure to secure your spot (limited seats): <a href="https://tinyurl.com/3y8ay2d6" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="">tinyurl.com/3y8ay2d6</span><span class="invisible"></span></a></p>
Headlines Africa<p>Africa: Continued Partnership to Enhance Pathogen Genomic Surveillance and Bioinformatics for Public Health in Africa: [Africa CDC] In a strategic move to bolster Africa's preparedness for future pandemics, the Africa Centres for Disease Control and Prevention (Africa CDC), in partnership with the African Society for Laboratory Medicine (ASLM) and with support from the Mastercard… <a href="http://newsfeed.facilit8.network/TJs8SK" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">http://</span><span class="ellipsis">newsfeed.facilit8.network/TJs8</span><span class="invisible">SK</span></a> <a href="https://journa.host/tags/PublicHealth" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PublicHealth</span></a> <a href="https://journa.host/tags/GenomicSurveillance" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GenomicSurveillance</span></a> <a href="https://journa.host/tags/AfricaCDC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>AfricaCDC</span></a> <a href="https://journa.host/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://journa.host/tags/PandemicPreparedness" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>PandemicPreparedness</span></a></p>
Hacker News<p>C. Elegans: The Worm That No Computer Scientist Can Crack</p><p><a href="https://www.wired.com/story/openworm-worm-simulator-biology-code/" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">wired.com/story/openworm-worm-</span><span class="invisible">simulator-biology-code/</span></a></p><p><a href="https://mastodon.social/tags/HackerNews" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HackerNews</span></a> <a href="https://mastodon.social/tags/C_Elegans" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>C_Elegans</span></a> <a href="https://mastodon.social/tags/ComputerScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>ComputerScience</span></a> <a href="https://mastodon.social/tags/Worms" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Worms</span></a> <a href="https://mastodon.social/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> <a href="https://mastodon.social/tags/OpenWorm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenWorm</span></a></p>
Christos Argyropoulos<p>Bless your heart <a href="https://mast.hpc.social/tags/Pubmed" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Pubmed</span></a> <a href="https://mast.hpc.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a><br><a href="https://academic.oup.com/bioinformatics/article/20/18/3363/202143?login=false" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">academic.oup.com/bioinformatic</span><span class="invisible">s/article/20/18/3363/202143?login=false</span></a></p>
naturepoker<p>Check this out, great timing! <br><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a> </p><p>Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment | Nature Methods<br><a href="https://www.nature.com/articles/s41592-025-02631-4" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">nature.com/articles/s41592-025</span><span class="invisible">-02631-4</span></a></p>
Christos Argyropoulos MD, PhD<p>Bless your heart <a href="https://mstdn.science/tags/Pubmed" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Pubmed</span></a> <a href="https://mstdn.science/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a><br><a href="https://academic.oup.com/bioinformatics/article/20/18/3363/202143?login=false" rel="nofollow noopener noreferrer" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">academic.oup.com/bioinformatic</span><span class="invisible">s/article/20/18/3363/202143?login=false</span></a></p>
Christian Meesters<p>Busy year:</p><p>- Workflow programming for Data Analysis on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>HPC</span></a> Systems (Course in Mainz in January): ✅ <br>- Same Course in Dresden (February) ✅ <br>- <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>SnakemakeHackathon2025</span></a> at the CERN in March: ✅ <br>- upcoming: <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenScience</span></a> Retreat (no hashtag, yet?) in April<br>- International Supercomputing Conference in June (so, <span class="h-card" translate="no"><a href="https://mast.hpc.social/@boegel" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>boegel</span></a></span>, I will be there, after all and hope to meet people from <span class="h-card" translate="no"><a href="https://fosstodon.org/@irods" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@<span>irods</span></a></span>, too ; will you be there folks from <a href="https://fediscience.org/tags/iRODS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>iRODS</span></a> ?)<br>- German Conference for <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>Bioinformatics</span></a> and NHR Conference in September</p><p>And I do not know whether this will be all. I have a nagging feeling there is more to come 😉</p>
Ming 'Tommy' Tang<p>My blog gets 30K views per month. The traffic is not huge but decent. I have limited time and am not an expert on every topic. I want to do an experiment. If you are an expert and want to write a tutorial on anything bioinformatics, please message me. <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>bioinformatics</span></a></p>
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