Tim Read

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

Seems I'm not good at Bactopia v4 progress updates!

Since my last update:
- Nextflow v25+ compatible
- Converted to nf-test
- nf-bactopia plugin released

If you are interesting in testing (very much appreciated!), I now have a dev build available here: github.com/bactopia/bac...

This is the sort of routine task that you would hope LMMs could do for you but it always seems that they can't

Pope Leo hits out at critics of global warming In his first major statement on climate change, the pontiff criticises those who minimise climate change.

This was a powerful speech by Pope Leo which built on Pope Francis’ teaching legacy.
He criticised those who “have chosen to deride the increasingly evident signs of climate change, to ridicule those who speak of global warming”.
It was a privilege to be in the room. www.bbc.co.uk/news/article...

It’s #MythBustingMonday.
Today’s myth: “Multiple vaccines at once will overload a child’s immune system.”
This idea is popular with anti-vaccine groups and also POTUS. But immunology, decades of research, and real-world data all say the same thing: it’s false. 🧵

Phenomenal. In my 10 year update of A Brief History, I make the point that in the first edition, not one disease had been successfully treated using gene therapy. Today that number is at least 7.

Good luck with your new adventure!

I had to triplecheck this because I didn't believe it...

All of the world's discovered reserves of fossil fuels = the same energy as just 5 days of sunlight hitting the Earth🤯

Solar power is basically unlimited🤷‍♂️

Partner fidelity and coevolution: Useful but not required for rapidly increased mutualistic benefits Evolutionary theory predicts that specialization between mutualistic partners is beneficial, limiting conflict and increasing the opportunity to evolve cooperative benefits through sustained reciproca...

Proud of the work in this new preprint from my postdoctoral research.

We used experimental evolution of mutualistically cross-feeding yeast to test how generalized interactions alter benefit evolution and opportunities for coevolution.

www.biorxiv.org/content/10.1....

Delighted to see the first version of our new ELife paper. A collaboration with Levi Morran, we show how an intact antibiotic resistance gene (mecA) changes the course of S. aureus evolution on a new host. Kudos to Michelle Su and Kim Hoang for making this happen.

elifesciences.org/reviewed-pre...

“Well I don’t like that study because it doesn't give me the result I want’

People reacting to the news that BLAST now outputs CSV files?

The graph from the California independent system operator showing the mix of electricity produced yesterday generated from imports, exports, wind, nuclear, fossil fuels and lots of solar and batteries.

Tweet from the Department of Energy saying wind and solar energy is essentially worthless when it's dark outside and the wind is not blowing. Basically showing the DOE doesn't understand energy.

During the day yesterday in California, >75%of all electricity was produced by renewable #energy, including solar.
After the sun went down, half of all electricity STILL came from renewables, including wind batteries, hydro, geothermal, etc.

A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise!

blast.ncbi.nlm.nih.gov/doc/blast-ne...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

In under 24h following the newly identified outbreak of #Ebola in the DRC, the virus has been isolated, sequenced and the virus sequence data made publicly available.
virological.org/t/the-16th-e...

One mother for two species via obligate cross-species cloning in ants - Nature In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...

Ok this is mad
"...an ant that lays individuals from two distinct species. In this life cycle, females must clone males of another species because they require their sperm to produce the worker caste"

www.nature.com/articles/s41...

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

Factcheck: 16 misleading myths about solar Carbon Brief factchecks 16 of the most common myths about solar power

The data shows that the future will be electric & renewable ... 🧪🔌💡☀️💨🌊🔋 The global energy transition is underway. And that is good for #Climate #Environment #PublicHealth #Economics interactive.carbonbrief.org/factcheck/so...

Fantastic news - congratulations!

Bactopia update!

Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.

If you're interested in testing please let me know here or at github.com/bactopia/bac...

Kennedy's case against mRNA vaccines collapses under his own evidence “This isn't scientific disagreement. It's either staggering incompetence or willful misrepresentation,” writes infectious disease physician Jake Scott.

The "data" package Secretary Kennedy used to bolster his argument for discontinuing #BARDA funding for #mRNA research doesn't support his argument. @jakescottmd.bsky.social lays it out in a must read for @statnews.com. www.statnews.com/2025/08/13/r...

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

Bactopia v4 - Overview & Help Wanted · Issue #628 · bactopia/bactopia Bactopia v4 Yo! Well, it is about that time! I am planning to release version 4 of Bactopia in the near future. With this version, Bactopia will introduce new and exciting things, but at the same t...

Howdy! I'm currently writing up version 4 of Bactopia!

Similar to previous major versions, I've started an issue on Github to track v4 progress. If you are a user of Bactopia and would like to help with feedback or with code, check out the following link:

github.com/bactopia/bac...

To say that "the data show these vaccines fail" in regards to the mRNA plaform is unforgivable.

For those of you that don't remember - this is the data from a SINGLE dose. In December 2020. So good I cried in grateful tears.

Helsinki goes a full year without a traffic death A city traffic engineer credits the success to lower speed limits and smarter design.

“Helsinki has not recorded a single traffic fatality in the past 12 months, city and police officials confirmed this week.”

City engineer credits lower speed limits and smart design.

I agree. #Helsinki #VisionZero

Carl Sagan explains how the ancient Greeks knew the Earth was round and calculated its circumference over 2,000 years ago.

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive chan...

The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻

www.biorxiv.org/content/10.1...

PO just confirmed that our 5th percentile R01 is not getting funded. Past NCI Payline at 4 percent. Cant believe it.

#microsky #plasmidsky #phagesky #phage

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

Neat approach: they found the putative digoxin effect by looking for prescriptions linked to a higher chance of GI infection in 1 million anonymous medical records