Arcadia Science

Whether you’re performing phylogenomic inferences, identifying structural differences and similarities between proteins, or doing high-throughput time-lapse imaging, we have some free, easily accessible tools and resources that may be helpful for you. 🧵

New pub from @ArcadiaScience 🧵 We found that C. smithii — a freshwater green alga — undergoes wild morphological transformations when grown on Marine Broth. Huge cells with mysterious wisp-like appendages. Here's what we saw. thestacks.org/publications/o… [1/9]

Just in time for Darwin’s bday! Interactive organismal tractability atlas from @ArcadiaScience for you to peruse as you consider species in the lab thestacks.org/publications/r…

Big day! We just dropped our 100th🎉 publication @ArcadiaScience! Check out our latest👇 Our first coherent Raman spectroscopy dataset in live fission yeast at subcellular resolution thestacks.org/publications/d… An evolution-informed bioprospecting framework to facilitate mining the tree of life for bio-utility thestacks.org/publications/p… A Bayesian strategy for collecting biological data to maximize information gain thestacks.org/publications/i…

1/6 We published a deep dive into what MSA Pairformer learns about evolutionary relationships. @yoakiyama et al. achieved impressive contact and variant fitness prediction with a fraction of ESM2's parameters; we wanted to understand the mechanism better. tinyurl.com/4ccn397z

We also released a free organism illustration library sharing high quality CC0 illustrations of 70+ organisms & viruses (including chlamy and sea squirts): x.com/thecrispress/s…

This spotlight is the second short video in our series highlighting organismal models. The first was on sea squirts: x.com/seemaychou/sta…

’Tis the season to be green 🌲 Our latest organism spotlight is Chlamydomonas reinhardtii — a tiny algae with a long history of punching above its weight in scientific discovery. Happy holidays! youtube.com/watch?v=cUscLH…

Check out our latest work at @ArcadiaScience on decomposing a neural network trained on Genotype-Phenotype data into interpretable and familiar quantitative genetics parameters. research.arcadiascience.com/pub/method-qg-…

How to transform UMAP from a black box into a glass box: by using a special type of deep network, we can now compute exact linear equivalents that reveal which features drive each point's position in the embedding. @ArcadiaScience [1/8]

Free, professional illustrations of research organisms! 🎨🐁🪼🪱 We compiled original vector/raster graphics of 70+ organisms & viruses into a CC0 library. All by @ArcadiaScience’s Audrey Bell Check it out & show us how you use them! research.arcadiascience.com/pub/resource-o… #scicomm #sciart

Introducing AutoOpenRaman, an automated, inexpensive microscope for Raman spectroscopy! 🧵 We recapitulated many features of expensive commercial systems using economical hardware and open-source software. @ArcadiaScience research.arcadiascience.com/pub/resource-a… [1/8]

Right now is the best chance the scientific community has ever had to end the artificial scarcity of academic journals. Check out my new op-ed urging @NIH @NIHDirector_Jay to disallow taxpayer dollars towards journal publication fees — something both publishers and scientists have played a role in perpetuating. The last day for public comment on this topic is Monday, Sept 15. It’s time to unleash science. Links in 🧵

we recently did our biggest icebox so far @ArcadiaScience -- we made the call to wind down our first/longest running start-up Trove. read about why & what we learned (and technical resources we released!). Quick 🧵👇 research.arcadiascience.com/pub/perspectiv…

Are you an ML researcher/engineer hoping to learn frontier biology? We’re looking for folks @ArcadiaScience to help build quantitative bio models w us. Our quest: find the MVP bio data required if it’s structured by evolution. Come for a stint to dig in! jobs.lever.co/arcadiascience…

Phenotypes often arise from linear + nonlinear genetic relationships. Neural networks should be great at modeling this. Results are mixed. Why? research.arcadiascience.com/pub/result-gp-… [1/11]

After many yrs building internally @ArcadiaScience, we're now able to partner more with others on cool organisms. You won't hurt my feelings if you don't read my post, but i will cut you if you don't watch our first organismal spotlight animation -- just skip to the bottom! 🧵

New website who dis arcadiascience.com

There's been a lot of movement on BioML recently @ArcadiaScience. Over the next couple of days, I'm going to cover our different efforts in defining the limits + potential of using ML to understand biology. First off: research.arcadiascience.com/pub/idea-phylo…

I’m hiring an applied machine learning engineer @ArcadiaScience - pls RT! jobs.lever.co/arcadiascience…