Seminar room with the projector displaying screenshots of the socials posts. My posts referencing benny hill and Heather Small’s Proud (one for the music of the millenium and Miranda fans out there). Winning post from Magdalena. Raymond on the left and David at the lectern

#AMGDMar26 social media prize runner up for yours truly. The content wasn’t strong enough to generate engagement this week. And you’ve got to be all killer and no filler when so many people have given up socials for lent. We do not let this slip, we go to Belfast. More of the same. We go again.

Bright sunshine with hazy clouds in the sky, view looking out over the car park towards old Joe and University of Birmingham campus

Bright blue skies above the medical school, small traffic including an sls van sporadic commuters dotted throughout the photo

View of the canals beside Snow Hill station, the water reflecting back blue skies and surrounding buildings

A late update for Day 5 of #AMGDMar26 on Friday our final day was blessed with beautiful sunshine in B15. A stark contrast to Thursday’s rain and strong winds.
Enjoyed wrapping up our top secret task: the disease outbreak scenario 🔬🦠

Magdalena is a white woman with short curly ginger hair and is wearing a bright yellow raincoat over a mint green top. She’s smiling at the camera with a mechanical bull statue of Ozzy the bull behind her

A white mug with a dark blue logo and orange writing. The logo shows a laptop screen with a DNA and microbes, and code underneath, the writing above reads Analysing Microbial Genomic Data

Saying goodbye to Birmingham after a brilliant week of learning about microbial genomic analysis at #AMGDMar26 🧫🧬 @unibirmingham.bsky.social with the best teachers and cohort!

And a special thank you to all of you for following along and helping me win the most coveted prize of the AMGD mug! ☕️

Coloured and separated phylogenetic tree with the fictional samples from infected patients highlighted red, suspects highlighted blue and the civilians as white

Phandango software plotting phylogenetic tree data and pangenome analysis

File path from the course. White background. Folder symbol/day3/task_arboretum/ then three folders with mash tree, parsnp and snippy based trees

#AMGDMar26 Back once again with the very jazzy outputs: colour coordinated (ooooo) and also alongside pangenome work using phandango (aaaaaa). Bairn’s phylogenetic arboretum with trees from a number (3) different coding origins

Nick is a white man with a beard and dark hair, standing in front of a projector screen showing a pandemic curve plot

Day 5 of #AMGDMar26 🧬 we wrapped up everything we learnt this week (a lot!) and completed our sci-fi quest by successfully identifying the suspects! 🥳

And got a fantastic seminar by @pathogenomenick.bsky.social about the real world applications of many of the tools we learnt about! 🦠

Final day (day 5) of #AMGDMar26 at @unibirmingham.bsky.social as @pathogenomenick.bsky.social gave an amazing talk on the applications of bacterial genomics in pandemics.

A red brick building against a cloudy grey sky

A whiteboard in the centre of a lecture room, a white man is writing on the whiteboard

Lines of code in black in a white background, a highlighted line reads “This analysis is totally hard-core!”

Day 4 of #AMGDMar26 🧬
Learning about the cutest way to analyse pangenomes (panaroo) 🦘 and a windy walk around campus while waiting for it to run @unibirmingham.bsky.social

An afternoon of phylogenetic trees in action @bacterioskeptic.bsky.social 🌳 and encouraging tools (thanks snippy!)

Phylogenetic tree on a white background, light reflecting off of one of the lines associated to a clade

#AMGDMar26 Bairn’s first phylogenetic tree, please ignore the reflection of the light at one of the nodes it’s not a clade experiencing a damascene intervention it’s purely the reflection from the ceiling.

University of Birmingham medical school big old brick/stone building with clock tower towards the back of the shot.

Small lecture room with a white title slide with the text Analysing Microbial Genomic Data. Day 4 part 1. David behind the lecturn on the right and Izzie on the left.

Day 4 of Analysing Microbial Genomic data #AMGDMar26
Working with Core and Pangenomes and building phylogenetic arboretums.
More overcast today and being battered by the wind but lovely conditions for coding!

Day 4 of #AMGDMar26 and on to pangenomes with @izziepotterill.bsky.social

I am unashamedly pleased about getting a Proclaimers song into a sequence alignment tutorial #AMGDMar26

A pack of stickers in front of a computer screen with blurred code. The sticker pack is branded MicrobesNG and the visible sticker at the front reads: Relax it’s just a phage

A fruit stall with a blue sky and clouds above, the building behind read Queen Elisabeth Hospital Birmingham

Day 3 of #AMGDMar26 🧬 learning about alignments through song lyrics, loops starting to make sense, a trip the market in the sunshine & shiny microbe stickers thanks to @helenmcneil.bsky.social @microbesng.bsky.social 🧫

Happy Bon Jovi Day, it’s day 3 at #AMGDMar26
Today was a belter, moving from the small sample work to the bigger datasets. Working through quality checks of assemblies, incorporating mlst and annotations. Big win for me getting the looped bakta annotation sorted. Alexa play Heather Small!

Bullring statue in Birmingham New Street, a large metal bull on the concourse of a train station, light coming through the ceiling panes.

Day2 of #AMGDMar26 brought back my struggles with for loops during PhD bioinformatics training. The morning very much felt like Dr Jon Tickle running on custard getting to grips with sequencing data, quality checks and trimming on a small scale. But by home time I was shovill’ing with the best of em

Midway through the #AMGDMar26 course and grateful to @helenmcneil.bsky.social of @microbesng.bsky.social for coming along and talking to attendees. Also gives them a much needed rest from hearing my voice!!!

Tidy desk set up. On the left; white coursework book and notebook with the course logo on the front. On the right the laptop with desert lock screen.

Brown envelope with red top secret stamp beside course notebook

Plenty of merch #AMGDMar26 including a tote bag, j’adore a tote bag. Notebook and laptop sticker all with the course logo on. #yesplease
Also looking forward to completing a top secret task. Applying skills to a fictional scenario. Once more. #yesplease

Central station main entry facing northbound toward the clock reading 05:10

Early start Monday morning to travel down to Birmingham for #AMGDMar26
Intentions of updating the timeline on the train were derailed by having minimal arm space and musical chairs. Nutrition provided by Greggs.

A blue sky with some clouds above a red brick building to the left and a grey building in the centre with the university of Birmingham crest

A computer screen showing a terminal inside a browser running fastqc on a number of samples

Day 2 of #AMGDMar26 🧬 was a lovely sunny day on campus @unibirmingham.bsky.social ☀️

Which alongside cake and the aim of saving the world (see Day 1) provided ample motivation for learning a whole lot about what to do with Illumina sequencing outputs 💻

Flat lay of a tote bag and booklet branded with the Analysing Microbial Genomic Data logo (a laptop showing a DNA double helix and microbes) and a sheet of paper that reads Human Bingo

A folded letter marked as classified with portions blacked out, suggesting the participants of the course must solve a fictional act of bioterrorism

Day 1 of #AMGDMar26 🧬 started with an icebreaker that was actually fun 😱!

And I cannot wait to live my science fiction dreams over the next few days 🤩

Oh and a tote bag?! Great start to the week!

Mags is a white woman and has short curly ginger hair and is wearing a yellow raincoat, she is smiling at the camera and pointing upwards with her left hand. She is pointing at a brick building behind her with a railways sign, university, and the university of Birmingham crest

Made it to Birmingham @unibirmingham.bsky.social for a week of microbial genomics fun! 🧫🧬💻 #AMGDMar26

Today is the start of the 5th Analysing Microbial Genomic Data course at @unibirmingham.bsky.social #AMGDMar26 - in the last three years we’ve trained nearly 80 attendees from six countries and multiple UK universities