Wytamma
@wytamma.bsky.social
Enjoying the little things like antibodies, ion channels and pip installs - technical biologist building tools and studying diseases ❤️🐢
One of the reasons I'm interested in local AI models is you're data can't be used for training - people say “I already put my data in onedrive so what's the difference to uploading it to an AI model?” Well one difference is that onedrive won't use your data to scoop you
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
nyti.ms
September 28, 2026 at 8:15 AM
One of the reasons I'm interested in local AI models is you're data can't be used for training - people say “I already put my data in onedrive so what's the difference to uploading it to an AI model?” Well one difference is that onedrive won't use your data to scoop you
Reposted by Wytamma
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences!
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
September 22, 2026 at 8:06 PM
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences!
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
Great to see more recognition for the hard working binfies ❤️ Well done Dan!
The #MicroSeq2026 Innovation in Bioinformatics Award goes to Daniel McKnight, who presented an automated pipeline for molecular diagnostic assay design and evaluation! Our field depends on creative, innovative minds like yours. Congratulations Daniel!
#MicroSeq2026
#MicroSeq2026
September 3, 2026 at 2:45 PM
Great to see more recognition for the hard working binfies ❤️ Well done Dan!
Reposted by Wytamma
Until next year, @royalfizzbin.bsky.social, @wytamma.bsky.social, @mozztacular.bsky.social, Asad, Mozammel, @bioelogy.bsky.social, and Clara out!
September 3, 2026 at 7:56 AM
Until next year, @royalfizzbin.bsky.social, @wytamma.bsky.social, @mozztacular.bsky.social, Asad, Mozammel, @bioelogy.bsky.social, and Clara out!
Reposted by Wytamma
✨ We hear you! Due to popular request, the deadline to submit an abstract to #MicroSeq2026 has been extended ONE MORE WEEK!
🚨 NEW DEADLINE (and this one's final): 11:59PM, Friday, August 7, 2026 🚨
Don't miss out! Register and get your abstracts in here 👉 trybooking.com/DNRBW
🚨 NEW DEADLINE (and this one's final): 11:59PM, Friday, August 7, 2026 🚨
Don't miss out! Register and get your abstracts in here 👉 trybooking.com/DNRBW
July 31, 2026 at 6:44 AM
✨ We hear you! Due to popular request, the deadline to submit an abstract to #MicroSeq2026 has been extended ONE MORE WEEK!
🚨 NEW DEADLINE (and this one's final): 11:59PM, Friday, August 7, 2026 🚨
Don't miss out! Register and get your abstracts in here 👉 trybooking.com/DNRBW
🚨 NEW DEADLINE (and this one's final): 11:59PM, Friday, August 7, 2026 🚨
Don't miss out! Register and get your abstracts in here 👉 trybooking.com/DNRBW
Reposted by Wytamma
Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma...
Thanks to Stephen J Bush for contributing this tutorial!
Thanks to Stephen J Bush for contributing this tutorial!
Intro to Makefiles
Interactive make tutorial: learn to use and create your own Makefile using a command-line interface in your browser.
sandbox.bio
July 2, 2026 at 6:45 PM
Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma...
Thanks to Stephen J Bush for contributing this tutorial!
Thanks to Stephen J Bush for contributing this tutorial!
Clockor2 v1.12.1 adds date-randomisation tests 🎉
Date randomisation is a permutation test for temporal signal: does the observed relationship between sampling time and genetic divergence exceed what we would expect if dates were unrelated to sequences?
Date randomisation is a permutation test for temporal signal: does the observed relationship between sampling time and genetic divergence exceed what we would expect if dates were unrelated to sequences?
July 1, 2026 at 10:35 AM
Clockor2 v1.12.1 adds date-randomisation tests 🎉
Date randomisation is a permutation test for temporal signal: does the observed relationship between sampling time and genetic divergence exceed what we would expect if dates were unrelated to sequences?
Date randomisation is a permutation test for temporal signal: does the observed relationship between sampling time and genetic divergence exceed what we would expect if dates were unrelated to sequences?
Reposted by Wytamma
📣Calling Australian/NZ ECRs and PhD Students 📣 Abstract submission and registration for #MicroSeq2026 opens July 6! Abstracts for both medium-length and lightning talks will be welcome.
June 25, 2026 at 6:27 AM
📣Calling Australian/NZ ECRs and PhD Students 📣 Abstract submission and registration for #MicroSeq2026 opens July 6! Abstracts for both medium-length and lightning talks will be welcome.
Reposted by Wytamma
New work on using transformers (using gene order) for tasks in genomic epidemiology:
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
May 6, 2026 at 8:35 AM
New work on using transformers (using gene order) for tasks in genomic epidemiology:
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
www.biorxiv.org/content/10.6...
We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
Reposted by Wytamma
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
May 5, 2026 at 8:06 AM
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
@lfeatherstone.bsky.social and I have just released v1.10.2 of clockor2.github.io 🎉 including several performance upgrades. Here we reproduce the results of McBride et al 2023, showing accelerated evolution of SARS-CoV-2 in white-tailed deer transmission clusters 🦌🦠
go.unimelb.edu.au/ydo2
go.unimelb.edu.au/ydo2
May 6, 2026 at 8:11 AM
@lfeatherstone.bsky.social and I have just released v1.10.2 of clockor2.github.io 🎉 including several performance upgrades. Here we reproduce the results of McBride et al 2023, showing accelerated evolution of SARS-CoV-2 in white-tailed deer transmission clusters 🦌🦠
go.unimelb.edu.au/ydo2
go.unimelb.edu.au/ydo2
Reposted by Wytamma
Thank you very much to the folks at Seqera for the opportunity to speak about new adventures in Bactopia.
Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...
Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...
May 1, 2026 at 7:34 PM
Thank you very much to the folks at Seqera for the opportunity to speak about new adventures in Bactopia.
Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...
Haha you'll have to wait for the video for the jokes, but for now the slides are available here: bactopia.io/impact-and-o...
Reposted by Wytamma
New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest
March 28, 2026 at 12:12 PM
New feature for PearTree - root-to-tip plots. Web version at peartree.live | desktop apps to follow at github.com/artic-network/peartree/releases/latest
Reposted by Wytamma
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
github.com
March 16, 2026 at 9:14 AM
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
Reposted by Wytamma
Wow, this is amazing @wytamma.bsky.social!
March 15, 2026 at 4:16 PM
Wow, this is amazing @wytamma.bsky.social!
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
March 14, 2026 at 5:32 PM
At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
Very happy to see Wasm gaining traction as a low barrier to entry alternative for programming thanks to the massive efforts by @quantstack.bsky.social 🎉 We're collecting Wasm resources for bioinformatics and beyond at wasmodic.github.io
February 25, 2026 at 10:52 PM
Very happy to see Wasm gaining traction as a low barrier to entry alternative for programming thanks to the massive efforts by @quantstack.bsky.social 🎉 We're collecting Wasm resources for bioinformatics and beyond at wasmodic.github.io
Reposted by Wytamma
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities.
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
This includes rich datasets for microbes, viruses & parasites associated with tropical diseases.
Explore the new datasets in the AlphaFold Database.
www.ebi.ac.uk/about/news/u...
AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
www.ebi.ac.uk
February 18, 2026 at 4:46 AM
Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
Reposted by Wytamma
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
bluesky-map.theo.io
February 8, 2026 at 10:59 PM
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Herple - Wordle for lizard people
Wordle for lizard people.
herple.wytamma.com
January 8, 2026 at 1:32 AM
Reposted by Wytamma
I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪
December 28, 2024 at 9:00 PM
I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪
Reposted by Wytamma
🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n)
#bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly
#bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly
GitHub - metagentools/graphbin-visualise-wasm-app: GraphBin Visualise WebAssembly App
GraphBin Visualise WebAssembly App. Contribute to metagentools/graphbin-visualise-wasm-app development by creating an account on GitHub.
github.com
December 2, 2025 at 1:38 AM
🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n)
#bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly
#bioinformatics #metagenomics #binning #webapp #pyiodide #webassembly
Workshop landing page with demos here -> wasmodic.github.io
November 29, 2025 at 1:18 AM
Workshop landing page with demos here -> wasmodic.github.io
Reposted by Wytamma
This was one of the best workshops I have ever been to.
I came out of it with a Wasm app for making pharokka/phold/phynteny's genome maps - available at gbouras13.github.io/phold-plot-w...
It runs the browser almost instantly - please give it a go with your phages of interest!
#ABACBS2025
I came out of it with a Wasm app for making pharokka/phold/phynteny's genome maps - available at gbouras13.github.io/phold-plot-w...
It runs the browser almost instantly - please give it a go with your phages of interest!
#ABACBS2025
November 28, 2025 at 4:23 AM
This was one of the best workshops I have ever been to.
I came out of it with a Wasm app for making pharokka/phold/phynteny's genome maps - available at gbouras13.github.io/phold-plot-w...
It runs the browser almost instantly - please give it a go with your phages of interest!
#ABACBS2025
I came out of it with a Wasm app for making pharokka/phold/phynteny's genome maps - available at gbouras13.github.io/phold-plot-w...
It runs the browser almost instantly - please give it a go with your phages of interest!
#ABACBS2025
Reposted by Wytamma
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
www.biorxiv.org
November 27, 2025 at 5:22 PM
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl