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New preprint: Cyanobacteria isolated from marine volcanic seeps display rapid sinking and robust, high density growth. Thanks to U Palermo and Two Frontiers Project, we got unique samples from Vulcano, Italy, where CO2 bubbles into the shallow ocean, 24-7! biorxiv.org/content/10.1101/…
Schubes retweeted
How do you publish this tree and claim it's a success???!!!
We are releasing Carbon: a crazy fast DNA model
Carbon is 275x faster than the next best model. So fast you can process the whole human genome on a single GPU in <2 days.
Here are the tricks we used:
When modelling DNA sequences a lot of the performance comes down to tokenizing the sequences in a smart way. BPE tokenizer struggle because there are no whitespaces and character (called base in DNA) level tokenizers waste a lot of compute on too many tokens.
Carbon is built with a unique tokenizer: we split sequences in chunks of 6 bases, but during both training and inference we can work with single base resolution. That's similar to having word tokens but resolving them at the character level. All possible thanks to the DNA tokens unique structure.
The architecture combined with the tokenizer makes the model 275x faster than the previous SoTA (Evo2) at this size.
We built an interactive demo so you can explore how the model can generate DNA sequences, investigate the structure of genes, predict the effect of mutations, generate and fold proteins and even reconstruct parts of the tree of life.
huggingface.co/spaces/Huggin…
Schubes retweeted
This tube is a library of bacteria with every single-base-pair genome mutation, all DNA-barcoded.🧪Growth + barcode sequencing = data on millions of mutations.
📄 Report: biorxiv.org/content/10.64898…
Retweet if you want more data, and read on if you want to use the library! 🧵
Schubes retweeted
An international coalition of scientists discovered a novel cyanobacteria strain adept at “eating” CO2 and sinking in water. It is a prime candidate for biologically-based carbon sequestration projects & bioproduction of valuable commodities.
wyss.harvard.edu/news/newly-…
Published version live today in AEM: journals.asm.org/doi/10.1128… alongside some commentary from @LindzBro @wyssinstitute wyss.harvard.edu/news/newly-…
It's been awesome to hear from researchers that are getting ahold of "Chonkus" and trying it out in their lab. Wishing you all the best, and don't hesitate to reach out. utex.org/products/utex-b-322…
Can we settle once and for all how to pronounce "-mycin" antibiotics?
100%Spectinomycin, Rapamycin.
0%'Spectinomy*i*cin' etc
0%don't care/ show me
3 votes • Final resultsTagging @izzymgm @ZijayTang @bradentierney @geochurch @mason_lab @MeclabU
@twofrontiers @krista_ryon @seedhealth @wyssinstitute @jkowitz and more- ongoing updates to the story forthcoming.
Lol also if you are interested in hearing me blubber about this on local radio have a listen (segment starting about 37:00) kpfa.org/episode/a-rude-awak…
Schubes retweeted
So @nanopore discovered something a few days ago - and it has to do with light. And they posted this image (sorry, too good not to share off the community). Yes, that’s 469% increased output. So, we decided to give it a shot and …
I would recommend opening up your laptop and cleaning the dust off your fans. Improves lappy cooling, and a sobering meditation on the lingering requirement for hardware and moving parts (!) and the fight against entropy.
Great opportunity for Climate-relevant projects looking to pursue translation from within academic labs!
Schubes retweeted
Five days left if anyone wishes to donate to my fundraiser! Making a ultra cheap turbidostat for use in experimental evolution. Fund go toward bringing these tools into the classroom. Every penny counts! 💚
experiment.com/projects/affo…

















