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James Zlosnik @jameszlosnik.bsky.social · 10d

Braga, Portugal.🇵🇹

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James Zlosnik @jameszlosnik.bsky.social · 13d

747 forever incredible indeed. Great flight yesterday.

James Zlosnik @jameszlosnik.bsky.social · 15d

Porto Pt3

James Zlosnik @jameszlosnik.bsky.social · 15d

Porto Pt2

James Zlosnik @jameszlosnik.bsky.social · 15d

Porto

Reposted by James Zlosnik

Samuel Lampa @smllmp.bsky.social · 20d

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".

Rewrite of Scicommander in Go with much improved algorithm | Living Systems_

livesys.se

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James Zlosnik @jameszlosnik.bsky.social · Sep 7

Budapest today

James Zlosnik @jameszlosnik.bsky.social · Sep 7

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

James Zlosnik @jameszlosnik.bsky.social · Sep 7

Yes. First time in Budapest was just there for a night. Much, much, better than I was expecting. Nice tree lined boulevards, lots of nice old buildings.

Not lost on me that some of those buildings and squares might be in the news in the future!

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James Zlosnik @jameszlosnik.bsky.social · Sep 6

Budapest this evening

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James Zlosnik @jameszlosnik.bsky.social · Jul 25

👇💯

Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25

My biggest, loudest job application advice:

WHY do you want this job? This SPECIFIC job? What about it interests you? What do you think of it? What can you bring to it?

I know this sounds obvious but a generic cover letter isn't doing you favours - really. *Show me you know the job!*

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Reposted by James Zlosnik

Dr Emma Hodcroft @firefoxx66.bsky.social · Jul 25

📢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!

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An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"

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Reposted by James Zlosnik

Andrew Rambaut @arambaut.bsky.social · Jul 15

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...

Pathoplexus | Pathoplexus July Update

Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

pathoplexus.org

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Reposted by James Zlosnik

Pathoplexus @pathoplexus.org · Jul 15

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/...

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Reposted by James Zlosnik

Pathoplexus @pathoplexus.org · Jul 15

🗓️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

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Screenshot of the July Update News article on the Pathoplexus website

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Reposted by James Zlosnik

sylvain Brisse @sylvainbrisse.bsky.social · Jun 12

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

Project manager: Genomic taxonomy of bacterial strains, epidemiological surveillance and antimicrobial resistance - Research

We are looking for a project manager to develop our activities around the genomic taxonomy of bacterial strains and the corresponding platform at https://bigsdb.pasteur.fr/. The project manager’s main...

research.pasteur.fr

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James Zlosnik @jameszlosnik.bsky.social · Jun 12

Yes that’s lovely 😊 . While if anyone deserved a longer healthy life he did, I am fortunate I recognized early on how special he was. Never took him for granted and loved every minute of the 14 years we were with him.

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James Zlosnik @jameszlosnik.bsky.social · Jun 11

Thank you Jaki, appreciate it. Seems odd to say, but those people are missing out. The pain is massive...but for good reason. They flood our life with joy and honest, uncomplicated, love in a way that, at least for me, other humans simply cannot.

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Reposted by James Zlosnik

Hadley Wickham @hadley.nz · Jun 10

Happy 18th birthday ggplot2! #rstats

Balloon wall art inspired by the ggplot2 hex sticker. The display features a hexagonal frame made of black balloons, filled with white balloons inside and surrounded by a background of light and dark blue balloons. A line graph with black balloon segments and round coloured nodes runs across the centre, and the word “ggplot2” is spelled out in black balloon letters below the chart.

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James Zlosnik @jameszlosnik.bsky.social · Jun 11

💯

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James Zlosnik @jameszlosnik.bsky.social · Jun 10

Thank you, appreciate it! No, there's no real preparation, just that awful numb feeling looking at the world without them in it any more. Made harder by the timing having to be my decision.

I had 14 very special years with him, that is indeed a great source of comfort.

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James Zlosnik @jameszlosnik.bsky.social · Jun 10

Thank you Dawn, appreciate it.
They all never be forgotten by us.

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James Zlosnik @jameszlosnik.bsky.social · Jun 10

I lost one of my cats, my best friend, on Saturday 💔💔💔. I knew it was coming, knew what to expect, but still seemed sudden and has been far, far, harder than ever expected. He was the best, kindest man in the world. The definition of a gentle-man. It's just devastating to know he's not there.

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Reposted by James Zlosnik

Nick Loman @pathogenomenick.bsky.social · May 22

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...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham

Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

www.birmingham.ac.uk

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Reposted by James Zlosnik

Dr Emma Hodcroft @firefoxx66.bsky.social · May 22

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! 👀👇🏻

Nick Loman @pathogenomenick.bsky.social · May 22

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...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham

Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

www.birmingham.ac.uk

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