The Wandering Shop

21 posts21 participants0 posts today

naturepokerDoes anyone know of a good tanglegram/cophylogram generator in Python? The only option I see is pretty minimal - not really up to par against the R version in features or visual quality. <a href="https://genomic.social/tags/phylogenetics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#phylogenetics</a> <a href="https://genomic.social/tags/dataviz" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#dataviz</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Luke PembletonCloud 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 😅 <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Luke PembletonThe 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">#bioinformatics</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>

Benjamin Carr, Ph.D. 👨🏻‍💻🧬<a href="https://hachyderm.io/tags/Genetic" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Genetic</a> data repo <a href="https://hachyderm.io/tags/OpenSNP" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenSNP</a> to self-destruct before authoritarians weaponize it The reason, according to <a href="https://hachyderm.io/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</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">#23andMe</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">#farright</a> <a href="https://hachyderm.io/tags/authoritarian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#authoritarian</a> regimes. <a href="https://www.theregister.com/2025/04/01/opensnp_shutdown/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.theregister.com/2025/04/01/opensnp_shutdown/</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>

Mark Ziemann 🇺🇦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. 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">https://genomespot.blogspot.com/2025/04/mitch-gets-upgraded-now-with-gene-set.html</a> <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/dataviz" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#dataviz</a>

naturepokerI'm thinking of submitting an Archaeal RNAseq project here.Anyone around here in touch with someone at Ultima Genomics? Their sequencing submission web form might have a permission issue :/ <a href="https://www.ultimagenomics.com/count-on-us/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.ultimagenomics.com/count-on-us/</a><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Pierre Lindenbaumasking 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">https://github.com/broadinstitute/gnomad-browser</a> for WGS)<a href="https://genomic.social/tags/database" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#database</a> <a href="https://genomic.social/tags/rnaseq" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rnaseq</a> <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Guillaume LouvelI'm writing way to much <a href="https://ecoevo.social/tags/awk" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#awk</a> code than I should...<a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

Bioconductor🎉 Announcing the EuroBioC2025 Sticker Design Winner! 🎉🏆 Winner: Chaima Hkimi🎨 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!Thanks to everyone who submitted a design. You’ll be able to pick up Chaima’s sticker at EuroBioC2025!<a href="https://genomic.social/tags/EuroBioC2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EuroBioC2025</a> <a href="https://genomic.social/tags/Bioconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioconductor</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/StickerContest" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StickerContest</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>

naturepokerCheck this out, great timing! <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment | Nature Methods <a href="https://www.nature.com/articles/s41592-025-02631-4" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41592-025-02631-4</a>

Christian MeestersBusy year:- Workflow programming for Data Analysis on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> Systems (Course in Mainz in January): ✅ - Same Course in Dresden (February) ✅ - <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SnakemakeHackathon2025</a> at the CERN in March: ✅ - upcoming: <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> Retreat (no hashtag, yet?) in April - International Supercomputing Conference in June (so, <a href="https://mast.hpc.social/@boegel" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@boegel</a>, I will be there, after all and hope to meet people from <a href="https://fosstodon.org/@irods" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@irods</a>, too ; will you be there folks from <a href="https://fediscience.org/tags/iRODS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#iRODS</a> ?) - German Conference for <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> and NHR Conference in SeptemberAnd I do not know whether this will be all. I have a nagging feeling there is more to come 😉

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.

Christian MeestersThe <a href="https://fediscience.org/tags/SnakemakeHackathon2025" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SnakemakeHackathon2025</a> just induced another collaboration for me!It is always good to work along with like-minded people, interested in <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleComputing</a>, <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> and <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

GHGAWant to improve your genomic variant calling pipeline? Join our webinar to learn about ncbench, a powerful benchmarking tool. We'll also cover other essential genomic benchmarking topics. Register for free: <a href="https://t1p.de/o4al3" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://t1p.de/o4al3</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/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#genomics</a> <a href="https://genomic.social/tags/variantcalling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#variantcalling</a> <a href="https://genomic.social/tags/ncbench" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ncbench</a>

grimmigesAlexandros Stamatakis' annual EMBO satellite <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a> workshop in Crete is open again for registration (free-of-charge, first-come-first-serve)This year: <a href="https://ecoevo.social/tags/biodiversity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#biodiversity</a> <a href="https://ecoevo.social/tags/genomics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#genomics</a> tools <a href="https://forms.gle/GRvPxCp2TnYdo8Po8" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://forms.gle/GRvPxCp2TnYdo8Po8</a>As Alexi is keen to point out: "... a good excuse to visit Crete?"

naturepokerWorking with newer ONT and pacbio data, I feel like minimum requirement for a proper raw data upload (to SRA and such) should be BAM calls at the very least, if not the raw signal files themselves. Either way, the fastqs just don't seem to cut it for meaningful in-depth research use. <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#bioinformatics</a>

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