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".

nice thing about summer holidays is getting the whole HPC to myself.

New thing to try is pinning posts!

ALRIGHT. PHEW. That took longer than I thought. But mstdn.science is running v4.4.3. If you want to have a look at what that means for you have a look at https://blog.joinmastodon.org/2025/07/mastodon-4.4/ For me, there is a new option to include a terms of service. Yaaaaay, just what I always […]

Testing a new version.

Still time to register for IMMEM XIV (17–20 Sept)! It covers everything from how genomics shapes resistance profiling to pathogen surveillance in a OneHealth context. Great programme, cool peeps -- Don't be a victim to FOMO. Programme […]

Surprisingly no one had made the triple j hottest 100 Australian songs of all time list on Spotify. Here it is. All the songs in order of the countdown. https://open.spotify.com/playlist/5AuCB7d2XqCwCjfVNJfBhg?si=6pykwQy2TqaRu9PcwKF0yA The full list […]

Please report any account that tells you that you need to verify your #mastodon account to continue using it through a private message. It is a scam. We do not require identity verification. Real staff accounts either have a special role badge on their profile or are verified through the […]

I'm back with this week's quiz. This time it's about R. A pirate's favourite statistics environment. https://forms.gle/GYT2qMiatRCsaNpKA This is a supplement to week 3 of https://www.futurelearn.com/courses/bioinformatics-for-biologists-analysing-and-interpreting-genomics-datasets/1/todo/173879

And a quiz for week 1 material https://forms.gle/4anTdaAb8b77vB1v9 which is a bit more general.

Bored? Try my bioinformatics quiz https://forms.gle/qykZnNFaeJknXk5f6

"Theory of Change" Wow. that's a lot of pretension to "making a plan"

Yeah… Science ain’t nothin’ to mess with Cash rules? Nah— Grants rule everything around me, G.R.E.A.M. Get the funding—dollar dollar scheme, y’all. I grew up on deadlines and tight scopes PI dreams soaked In lab coats and peer review quotes Scholar life—writing late in the night Jargon so dense […]

S. Typhi isn't a thing. Stop it. Salmonella Typhi if you must.

immem hackthon registration closes 31st May. https://www.escmid.org/congress-events/immem-xiv/12th-microbial-bioinformatics-hackathon/

@happykhan boosting this to say that I finally found that opencollective also takes credit cards, and that allowed me to set up a monthly contribution for mstdn.science. Previously I had sent one-off donations via bank transfer, and that costs about as much in bank fees (and €->£ conversion) as […]

Welcome to #abphm25

It all begins for #abphm2025 with keynote from Johanna Hanefeld (RKI).

Eurovision is always a fun stress test for the fediverse. Across #esc, #eurovision, #esc25, and #esc2025, over 15K posts have been been made today. For comparison, 863 posts have been made in another trending hashtag, #caturday.

It's honestly insulting people ask to come visit me and have me teach them bioinformatics in a matter of weeks and months, when my expertise is something that took years.

UK gov announced changes to immigration policy. Not sure what the implications are for scientists/ postdocs moving to the UK. UK science is greatly enriched by having good talent move here. Details are scarce in their white paper but increasing number of years to settlement from 5 to 10 will be […]

Is anyone writing down what is actually happening? I get the feeling that people will look back and believe whatever history the victors will write, and there isn't many other sources to contradict that.

`btop` is beautiful. Why did I suffer with mere `htop` for so long? Not that htop wasn't itself a huge leap/bound above regular-top, but.

Now Running v4.3.8. let me know if there's any snags. We run at a shortfall in terms of funds, so any contributions are welcome (you can review our spending and make a contribution here: https://opencollective.com/mstdnscience)

i have waaaay too many meetings for someone who doesnt like talking.

we are hiring - Senior Operations and Programme Manager […]

i used to find the music video for Aphex Twin - Come To Daddy really creepy, but now I feel it just reflects the feeling of living in England.

Last chance to register for ABPHM. Closes today. https://coursesandconferences.wellcomeconnectingscience.org/

Huge disparity in genomic data: We support all efforts to increase the genomic surveillance of pathogens on a global scale as dynamics differ locally: what happens in one place does not translate to another and high-risk clones can emerge anywhere […] [Original post on mstdn.science]

Our latest preprint is out describing http://amr.watch – a platform for monitoring AMR trends from global genomics data. Supporting all WHO priority pathogens (2017), http://amr.watch summarises the geographic and temporal distribution of genotypic variants (e.g. STs) in the context of AMR to […]

Omg. Nicole is a menace.

Merging a pull request afternoon before long weekend. What could possibly go wrong.

It's really really hard to help people do research computing work (run pipelines, analysis, visualise) when they don't know any programming or scripting via bash perl python, R, etc. I don't know why there's so much resistance to learning This. It's apparently unreasonable for me even to ask.

"exceeds expectations" doesnt really say whether something is bad or good.

I think Dune (first book) would do really well as a telenovella.

here's a recording of a seminar i gave today. Using containers (docker) for bioinformatics software https://youtu.be/eBy-W2bUklw?si=A1mNYiKSe3k1xyO5 I cover. ✅ What is containerisation and how it helps make analyses reproducible and portable ✅ Key differences between Docker and Singularity ✅ […]

what'd ya'll think of the new fund raising page https://opencollective.com/preview/mstdnscience

DONT PUT your masters thesis as an ATTACHMENT to a job advert. If you must, have a link to a dropbox or similar in the cover letter.

My origin story?

Seen a few dapper gents at #microbio25 in waistcoats and good shoes. Well In. Maybe there's a market for an MSoc necktie/bowtie @MicrobioSoc

Nice video about Marjory Stephenson https://youtu.be/hr5b9f8hIVk?si=aIl_8U_-wXBwnCMw

Come find me at #microbio25 if you would like a sticker !

#microbio25 come find me at my poster today A067.

Is any of this LLM stuff actually helping people regarding accessibility. I never hear about that. Just about making little cartoons .

I'll be at the UK microbiology society annual conference next week, come say hi. https://microbiologysociety.org/event/annual-conference/annual-conference-2025.html

zenodo is down?