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As far as i know the SLURM scheduler was named after the drink in futurama.

It appears today is the one sanctioned day of summer in the UK. You have my permission to take the day off.

You need a phd to admin a moodle. My god.

TGIF team. How we all doing.

It's caturday. Post some mother liking cats.

Time for some database spring cleaning . Here are my top tips for mastodon admins! Index bloat is your #1 enemy. Federation churn (constant insert/delete cycles) destroys B-tree indexes fast. Run this on your Postgres server: REINDEX TABLE CONCURRENTLY public.statuses; Repeat for […]

We're now running mastodon 4.5.9 As always, let me know if things are not working as expected. If you have some spare dosh, please donate to https://opencollective.com/mstdnscience All proceeds go to running the server, our books are open for your scrutiny.

💡 Support mstdn.science with a Financial Contribution! 💡 mstdn.science exists through contributions by folks like you. If you're not skint from the season's festivities, consider making a regular contribution to https://opencollective.com/mstdnscience . If we can manage another £60 / month, the […]

Could some clarify what it means go medieval on ones ass? Like specifically what would that entail and what equipment would be needed ?

Oh yeah. Support the instance. https://opencollective.com/mstdnscience

omg. I was using MS word --- and i forgot to save a doc! I have become too lazy with autosaving via google docs. !!

BRIG v1.1.1 release. There's some minor quality of life changes but the key thing is fixing the GC Skew and Content graphs for small reference sequences (plasmids), from the chunky and blocky histogram, we now have a much smoother solution. Download from […] [Original post on mstdn.science]

Host read removal sounds simple. It's not. 🧫Ep. 151 of hashtag#microbinfie: we talk with Bede Constantinides about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2 […]

Been working on a browser version of BRIG. No install. Interactive. Looking for beta testers; message me if you're interested.

Bye bye research fish

We just uploaded the 150th episode of the #microbinfie podcast, scheduled for Thursday, where we blow your mind with vibe coding. I can't believe we have actually made it this far. 🍻 To the next 150 episodes 🥂 https://soundcloud.com/microbinfie

Nearly 90% of AMR pathogen genomes come from high-income countries.109 participants from 52 countries meeting in Addis Ababa to close this gap. www.amrsurveillance.org #AMR #HealthEquity #Genomics #AMRSurveillanceAddis

Reporting from the AMR Surveillance Convening at Africa CDC, Addis Ababa. Opening message was direct: the surveillance gap isn't about knowledge anymore, it's delivery and financing. Africa carries ~21% of the global AMR burden. Recap of Day 1 from www.amrsurveillance.org #AMRSurveillanceAddis

Sentinel site session was the most grounding. Surveillance fails when it's extractive — data goes up, nothing comes back. Labs engage when it improves their own practice. www.amrsurveillance.org #AMRSurveillanceAddis

Four national stories. Philippines: 38 years of AMR surveillance, now adding WGS. Uganda: 16 to 43 sites. Pakistan: building a genomic strategy. Brazil: mapping labs nationally. Start small, invest in quality, build government ownership. #AMRSurveillanceAddis Day 1 of www.amrsurveillance.org

Last session pushed beyond bacteria. Azole-resistant Aspergillus linked to agricultural fungicides. C. auris likely accelerated by climate change. Almost no global capacity for fungal genomic surveillance. AMR is bigger than bacteria. www.amrsurveillance.org #AMRSurveillanceAddis

We're now running mastodon 4.5.7 As always, let me know if things are not working as expected. If you have some spare dosh, please donate to https://opencollective.com/mstdnscience All proceeds go to running the server, our books are open for your scrutiny.

BRIG v1.0.0 Released — BLAST Ring Image Generator This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1. BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]

Do you get emails like this? "Reminder: Complete the Harassment in Higher Education Training" The subject line always gives me the impression that the training is in how to Harass better. Luckily it's about how to stop this behaviour.

Whole genome sequencing (WGS) underpins public health surveillance, AMR monitoring, outbreak investigation, and comparative genomics. But what defines a trustworthy genome assembly? We’ve developed guidance outlining minimum QC standards for short-read bacterial genome assemblies See […]

https://www.bbc.co.uk/news/articles/c8e50x1r237o Why is no one really saying anything?

When I was a kid I always ordered my steak well done. Because why wouldn't you want it done well?

I'm talking tomorrow at the festival of genomics and biodata in London. https://festivalofgenomics.com/london/ If y'all around, would be great to meet up.

unrelated but related, emoticon reactions to emails. like who thought that was a good idea..

Someone personally invites me to apply for something. I send the application to the person handling it. No acknowledgment of receipt. Yeah, I guess that’s just how everything works these days.

bluesky's "starter packs" are supposed to come in the next mastodon version (4.6). which i think, will solve the empty feed onboarding problem -- which is probably the most off putting thing about mastodon.

RE: https://mstdn.science/@happykhan/115847639896793459 Updated to version 4.5.3 now. When you click the Boost button on any post, you will have the option to Quote it instead. For more changes see : https://blog.joinmastodon.org/2025/11/mastodon-4.5/

Good day. I'm doing some new year clean up. The preview cards for links will likely disappear, but will eventually come back.

Happy new year gang. All the best.

💡 Support mstdn.science with a Financial Contribution! 💡 mstdn.science exists through contributions by folks like you. If you're not skint from the season's festivities, consider making a regular contribution to https://opencollective.com/mstdnscience . If we can manage another £80 / month, the […]

@FediTree 🎄

What are airlines aversion to special characters? how much damage can one hyphen do?

yes, yes. i will do the new update soon. Quoting posts. hooooow exciting!!

Folks been asking for a searchable catalogue for microbinfie podcast. With a 147 episodes, and 78+ guests its getting hard to find episodes of your interest. anyway, i wrote a catalogue https://www.happykhan.com/microbinfie see all our lovely guests at https://www.happykhan.com/microbinfie/guests

If you are chairing a meeting, and it's not going ahead. You need to tell people and/or take it out of the calendar. It shouldn't be ME as the participant, always having to follow up if that recurring meeting that no one likes is happening or not.

Have to say. This is the only place where real people post. (Honourable mention to linkedin :oh_no_bubble: ).; Cheers big ears.

🚀 Should You Start with Nextflow in 2025? If you're working in bioinformatics, computational biology, or data science, you've probably seen Nextflow—so the question is: is it still worth adopting now? We recently recorded a three-part debate on this topic. 🎙️ 👉 […]

Come see my poster at IMMEM Poster 151. 🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq). ⚙️ SpecCheck – an open-source command-line tool that applies these standards […] [Original post on mstdn.science]

If you're at IMMEM. please come by and see "my" poster on vaccines.watch Otherwise please read the preprint. https://www.biorxiv.org/content/10.1101/2025.06.13.659488v1

Just dropped: #microbinfie Pathoplexus Part 1! Join Lee & guest Clint (and me) as we deep-dive with Emma Hodcroft, Theo Sanderson & Arthur Shem Kasambula about Pathoplexus […]

I thought professors were really into moving furniture, but apparently that's not what it means when they are "holding a chair".