iiinova — where your digital self keeps evolving

Reposted by Broncio Aguilar-Sanjuan

sylvain Brisse @sylvainbrisse.bsky.social · 30/11/2025

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

doi.org

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

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University of Oxford @ox.ac.uk · 13/12/2025

Christmas trees around Oxford 🎄 📷 Instagram | Lucies_Oxford_Camera, Dr Laura Varnam, Spiralling_Oxford & Lady Margaret Hall

A large, illuminated Christmas tree stands in a courtyard at night in front of the historic architecture of Magdalen College, Oxford, with a clear sky and a bright star visible above.

Illuminated Christmas tree at night in the courtyard of Univ with stained glass windows.

A beautifully illuminated Christmas tree stands near the Radcliffe Observatory, next to a statue in a fountain, set against the evening sky.

A Christmas tree illuminated with blue lights stands in front Lady Margaret Hall at night.

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 12/12/2025

I just published Why Every Website Needs a robots.txt File (And What Happens If You Ignore It) medium.com/p/why-every-...

medium.com

Why Every Website Needs a robots.txt File (And What Happens If You Ignore It)

What the heck is a crawler or bot? 🤖

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The Carpentries @carpentries.carpentries.org · 17/11/2025

Upcoming community sessions this week carpentries.org/community/ev... Events are in UTC Time : Having Difficult Conversations 19 Nov 14:00 Ten Years of Library Carpentry 19 Nov 16:00 HPC Carpentry Community Call 20 Nov 12:00 & 22:00

carpentries.org

Community Events

There are many opportunities to join community meetings, subcommittees and debriefing sessions. Find links to them on this Etherpad, and subscribe to the Google calendar below or use this ics feed to…

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Fabian Spoendlin @fspoendlin.bsky.social · 16/10/2025

Check out our new paper in Nature Machine Intelligence on predicting the structural flexibility of antibody and TCR CDR loops. Although methods like AlphaFold have transformed static structure prediction, capturing conformational dynamics remains a challenge.

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Reproducible Research Oxford (RROx) @rr-ox.bsky.social · 16/10/2025

🤔 Do you want to learn data analysis & computational skills but not sure where to start? 💡 Why don't you try one of our Carpentries workshops? 📝 Read our blogpost with highlights from our latest workshop on Python and Git and find out more. rr.ox.ac.uk/article/soft... #Carpentries #Oxford #Python

rr.ox.ac.uk

Software Carpentries - workshops and tutor training

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 09/10/2025

Just for fun. I just published a blogpost on how to resize and crop multiple images programmatically medium.com/@ba13026/res... #imageediting #photography #WebDevelopment

medium.com

Resize and crop multiple images programmatically

Quick preamble (skip if you want)

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Reposted by Broncio Aguilar-Sanjuan

The Carpentries @carpentries.carpentries.org · 29/09/2025

Upcoming community sessions next week carpentries.org/community/ev... Events are in UTC Time : 📣 Workbench Transition Coworking 29 Sep 08:00 & 18:00 📣 US Midwest Community Call 1 Oct 17:00 📣 HPC Carpentry Community Call 2 Oct 11:00 & 21:00 📣 CarpentriesOffline Community Call 3 Oct 13:00

carpentries.org

Community Events

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 26/09/2025

Good follow-up talk after attending #CampyUK for the last two days 🦠🦜

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 25/09/2025

Very pleased to have become a certified #Carpentries instructor. Thank you very much to @rr-ox.bsky.social and @sheppardlab.bsky.social for their support. I will be able to assist The Carpentries' mission to build global capacity in data and computational skills for open and reproducible research.

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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025

Carrying on the Peru studies, Kerry Cooper details the introgression of RE-cmeB gene from C. jejuni into C. coli. This gene is involved in multi-drug resistance and found more commonly in commercial chickens 🐓🇵🇪 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025

Ben Pascoe @benizao.bsky.social @sheppardlab.bsky.social shining a light on C. coli - although less common than C. jejuni, it has higher levels of AMR. His work in Peru highlights the importance of this pathogen in LMICs due constant exposure with backyard livestock and antibiotic use 🇵🇪 #CampyUK2025

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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025

Our fantastic @sheppardlab.bsky.social DPhil student Madison Goforth gives us a global overview of Campylobacter source attribution and the spread of AMR 🌎💊🌎 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025

#CampyUK2025 organiser Dr Fran Colles @fran-co001.bsky.social outlines findings from the soon to be published PATH-SAFE report - Campylobacter cases and fluoroquinolone resistance are on the rise, with most of these infections coming from chickens 🐓💊 @sheppardlab.bsky.social

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CampyUK2025 @campyuk2025.bsky.social · 25/09/2025

Keynote speaker Prof Dave Kelly is providing us with some Campylobacter biochemistry for the first talk for day 2 of #CampyUK2025 ⚛️🧪 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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Gauri G @gaurig03.bsky.social · 24/09/2025

Genomic epidemiology of Campylobacter in England and emergence of invasive Campylobacter ureolyticus in England @ukhsa.bsky.social @campyuk2025.bsky.social @amydouglas.bsky.social

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Panel discussion time - what are the current and future Campylobacter challenges? Speakers from the Food Standards Agency, British Poultry Association, University of Reading and Christian Medical College 🗣️🗣️ #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Final talk of the day from the fabulous Marian Dawkins representing @ox.ac.uk . Interdisciplinary methods tell us that chickens infected with Campylobacter behave differently to those which are not 🐓‼️ #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

@microbiolocris.bsky.social presents her findings of C. jejuni ST-52 emergence and survival from farm to fork in the Danish food chain 🍔🍴 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Are antibiotics a dead parrot? 🦜Prof Aidan Taylor kicks off the ‘From farm to fork’ session discussing Campylobacter AMR and vaccine development 🧫💉 #CampyUK2025 @microbiologysociety.org @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Another speaker sponsored by @microbiologysociety.org , Prof Sitara Ajjampur talks about age and exposure to infected poultry in backyard chicken flocks as determinants of Campylobacter infections in children in rural south India 🐓🇮🇳 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

@sheppardlab.bsky.social collaborator Francesca Schiaffino, sponsored by @microbiologysociety.org explains patterns in persistent Campylobacter infections in LMICs, using data from Peru to investigate complex long-term carriage 🐓🇵🇪 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

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Reproducible Research Oxford (RROx) @rr-ox.bsky.social · 24/09/2025

Pleased to have hosted our workshop “Python Essentials with Git for Data Analysis” at the Weston Library in Oxford — a superb venue for two great days of learning. A huge thank you to our organisers, instructors, and helpers for making this workshop possible! #Oxford #Reproducibility #Carpentries

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

A warm welcome from the head of @biology.ox.ac.uk Prof Martin Maiden and a thank you to our sponsors @microbiologysociety.org, Don Whitley Scientific and @genewiz.bsky.social

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Our very own @sheppardlab.bsky.social DPhil candidate Amy Douglas representing the @ukhsa.bsky.social giving us some Campy stats 🤩🤩🤩 #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

Fascinating talk from keynote speaker Dr Christine Szymanski about how Campylobacter jejuni has evolved to colonise and survive the breastfed infant gut #CampyUK2025 @ineosoxford.bsky.social @biology.ox.ac.uk

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CampyUK2025 @campyuk2025.bsky.social · 24/09/2025

And we’re off! Excited for a day full of all things Campy. The Sheppard lab @sheppardlab.bsky.social welcomes everyone to CampyUK, the first conference in the new Life and Mind Building @ox.ac.uk

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Reproducible Research Oxford (RROx) @rr-ox.bsky.social · 15/09/2025

Pleased to announce our in-person workshop on Python and version control with Git (Beginner to Intermediate). 22-23 Sept 2025, 9.45am-4.30pm at Weston Library. Places are free and open to all University of Oxford members. Register here: forms.office.com/e/pyPh9pcKcM #oxford #reproducibility

forms.office.com

Microsoft Forms

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Sheppard Lab @sheppardlab.bsky.social · 02/05/2025

Sheppardlab is organizing the Campylobacter UK conference in Oxford in Sept. Register and submit abstracts: campyuk.web.ox.ac.uk/home @OxfordBiology ; @IneosOxford

campyuk.web.ox.ac.uk

Home

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Sheppard Lab @sheppardlab.bsky.social · 05/06/2025

Punting rained off…

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Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 22/04/2025

Work led by Alex Greenshields-Watson and Parth Agarwal, and initially began by @saraharob.bsky.social. Many contributions from Henriette Capel, Gemma Gordon, @fspoendlin.bsky.social, Yushi Li, @broncio.bsky.social, Fergus Boyles, and Benjamin Williams. Project supervised by Charlotte Deane

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 22/04/2025

Happy to share the incredible work on AI-based antibody numbering by my friends and colleagues from the Oxford Protein Informatics Group @opig.stats.ox.ac.uk This is a significant leap away from traditional rule- and HMM-based numbering and into TCR, VHH/VNAR immune proteins.

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Reposted by Broncio Aguilar-Sanjuan

Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 22/04/2025

We have released the successor to ANARCI - ANARCII - a suite of Seq2Seq language models trained to number antibody (or TCR) sequences! Read the paper: biorxiv.org/content/10.1... Play with the webtool: opig.stats.ox.ac.uk/webapps/sabd... Documentation and codebase: github.com/oxpig/ANARCII

github.com

GitHub - oxpig/ANARCII: A language model suite for numbering antigen receptor sequences.

A language model suite for numbering antigen receptor sequences. - oxpig/ANARCII

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Bioinformatics Advances @bioinfoadv.bsky.social · 02/04/2025

🧬Available now in Bioinformatics Advances: "AntiFold: Improved structure-based antibody design using inverse folding" Find the full paper here: doi.org/10.1093/bioadv/vbae202 #AntibodyDesign #ProteinEngineering #MachineLearning Authors include: @broncio.bsky.social @opig.stats.ox.ac.uk

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Broncio Aguilar-Sanjuan @broncio.bsky.social · 23/03/2025

JP Morgan's return-to-office mandate made headlines recently. It's not alone, other employers have been trying to crack down on hybrid work. This has stirred a debate on flexible work and its impact on productivity, diversity, employment satisfaction and retention. Here's an article on the topic.

stackoverflow.blog

Are remote workers more productive? That’s the wrong question. - Stack Overflow

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