Braga, Portugal.🇵🇹

747 forever incredible indeed. Great flight yesterday.

Porto Pt3

Porto Pt2

Porto

Registered too late for a poster for @escmid.bsky.social #IMMEMXIV but happy to discuss SciCommander with anyone interested 😊 See: livesys.se/posts/rewrit... Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".

Budapest today

Seen in Budapest… “Scientists are human too”. Indeed we are!

Budapest this evening

👇💯

📢New job posting!📢 Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬 My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on! 1/5

Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...

In an awesome new feature, you can now use the ‘Tools’ button to send sequences from Pathoplexus to other analyses and visualizations - like maps or Nextclade! Have a tool that would be worth including? See our docs! pathoplexus.org/docs/how-to/... 5/9

🗓️As we close in on 11 months of Pathoplexus, we’re pleased to announce many new direct sequence uploads and some exciting new features that expand Pathoplexus’ utility! 📰 You can see our full News Item here: pathoplexus.org/news/2025-07-14-july-update 1/9

The BIGSdb-Pasteur project, running under my supervision since 20 years, is looking for a project manager - great opportunity to contribute to this high-profile international resource in the field of reference strain taxonomies, genomic epidemiology and antimicrobial resistance surveillance

Happy 18th birthday ggplot2! #rstats

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Excited to announce the start of ARTIC2! 🎉 ARTIC2 builds on the success of ARTIC aiming to make sequencing more equitable and accessible. 🤝🧬 EVE Group at @swisstph.ch is a key team member - we'll be helping make sequences easier to store and share via Loculus & @pathoplexus.org ! 🌎 More below! 👀👇🏻

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

This is Canada — and we decide what happens here.

"One thing that happens when you have that much lying is that people begin to ask, is anything true? How do we know whether anything is ever true?" Don't let Trump's lies fatigue you or turn you cynical. @anneapplebaum.bsky.social joins @sarahlongwell25.bsky.social on the The Focus Group pod:

A person who views their health with a scientific lens is advantaged. Wellness grifters hold less power over those who can see through their charades.

Excellent interview. For anyone in Canada, well worth a listen.

It’s time to protect our values as Canadians. That means more doctors and hospitals in our public health care system, protecting our lands and waters, and standing up for our Charter of Rights and Freedoms.

"We infer that the earliest aerobic bacteria emerged in the Archaean, predating the GOE by 900 million years." Oxygen tolerance may have been a prerequisite for, rather than a consequence of, the evolution of oxygenic photosynthesis www.science.org/doi/10.1126/...

The tragedy of young science trainees being driven out of research is incredibly upsetting. Doubtful they’ll ever find their way back and among them are the discoverers of future cures for cancers and other intractable diseases.

Super happy to see the new @nextflow.io training videos up online 🎉 This is a brand new course for beginners, called #Hello #Nextflow - we've run it a few times and the feedback so far has been great! Material is at training.nextflow.io and videos are on YouTube: www.youtube.com/watch?v=G3CV...

@11tulips.bsky.social @dennowayne.bsky.social @docjanicel.bsky.social @davidhemond.bsky.social @jakichantler.bsky.social & all A transatlantic cri de coeur, directed at the Democrats. Just to give an idea of feelings in Europe. Worth watching the full speech by French senator Malhuret, 8+ mins.

For microbiologists, if you don't know of this it is well worth your time to go and visit the website to read up on this incredible 37 year laboratory experiment in evolution. Huge achievement by all involved.

🦘✂️ Thanks to @cziscience.bsky.social , @wytamma.bsky.social and I are writing the next version of the Snippy bacterial variant calling pipeline. We want your input on what features s it will have. Please fill out this (longish) survey to help make Snippy great again! forms.gle/YJP6WQjsk8KK...

Notice how the king doesn’t mind the dress code

Great story. Nice inclusion of recent work by @greyson.bsky.social 👍 @bcchresearch.bsky.social

And to think we could have had a sane, serious government run by an intelligent person who would have acted in the best interests of Americans, and not Vladimir Putin.

Clay Bennett nails it.

"We’re witnessing the self-sabotage of the United States" from @davidfrum.bsky.social www.theatlantic.com/politics/arc...

My editorial simultaneously published in all of @asm.org's journals addresses the ongoing effort by the administration to halt efforts to diversify science. It should be obvious from ASM Journals' efforts over the years, but we aren't fans journals.asm.org/doi/10.1128/...

I’ve seen children die of -influenza -COVID -pertussis And wouldn’t wish those experiences on anyone. Know what these things have in common?! Effective vaccines that save lives.

"In 2022, I saw tiny workshops that made drones out of what looked like cardboard and glue. In 2024, Ukrainian factories produced 1.5 million drones, and this year they will make many more. Soldiers in underground control centers now use bespoke software to hit thousands of targets every month"

This is the best summary of the current geopolitical situation I have seen. Sir Alex Younger (head of MI6 from 2014-2020) is a genuine expert and provides concise insight into a complex situation. Not just some talking head with an opinion. Really worth watching. www.youtube.com/watch?v=I9pL...

Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important

➡️ NIH grants in '23 included $26B of direct costs and $9B of F&A = 26% of total costs or 35% of total direct costs. These are LOW overhead rates for any R&D-intensive industry. Academic biomedical research is an efficient bargain. ➡️ Every $1 of NIH support generates ~$2.50 of economic activity.

"The increase to Musk's wealth since Trump was elected president three months ago is greater than all of the American aid given to Ukraine over the last three years."-- @timothysnyder.bsky.social

I’m George Takei and I approve of this message.

Vance’s grotesqueness aside, the whole thing is one of the most horrific acts of betrayal ever committed by a democratic state against another. Just a moral abomination and a permanent stain on everyone who supports it

🇺🇦🇺🇦🇺🇦

New pre-print from folks @ Copenhagen University Hospital: 🔬 28-month WGS surveillance 🦠 7,760 patient infections 📊 27.1% genetically related, 69% w/ epi link 💰 €1.25M net savings/year if acted upon/prevented! #IDSky more great evidence for WGS for IP&C 📄: www.medrxiv.org/content/10.1...

I stand with Ukraine 🇺🇦.