Ben Braverman

If you’re a fan of DIY lab equipment, you’ll love the phenotype-o-mat, a customizable DIY 96-well plate imager from @ArcadiaScience that you can now build for only $400 🧵 1/7 protocols.io/view/building-…

Everything's open: the plate map generator, Opentrons scripts, 3D print files, and a protocol walkthrough. Built for the Cayman kit + OT-2, but adaptable to similar ELISA workflows. Code: github.com/Arcadia-Scienc… Try it out and let us know how it goes! [6/6] ✨

We validated it on Chlamydomonas reinhardtii lysates, cleanly distinguishing a His-tagged atpB strain from an untagged control. One lesson: always run a dilution series for new sample matrices — lysis buffer components can interfere with binding even at 1:5. [5/6]

Scaling up ELISA-based protein quantification? We built an automation workflow for the Cayman His-tag detection ELISA kit using the Opentrons OT-2 liquid handler. 🧵 Read the pub: thestacks.org/publications/r… [1/6]

AI agent loop controlling our automated Raman microscope - from acquisition to stage movement to online analysis. It does a quick scan, then re-acquires spots with the best signal, and finally finds the most distinct spot and does an in-depth acquisition @ArcadiaScience

@wasserstein_rao looks awesome, wonder if anyone has done this for opentrons?

Using claude code to directly control a liquid handling robot is such a crazy experience

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

@AdrianoAguzzi good to know, I'll look into using this for custom 24 well baffle plates. I assume getting a similar depth to a standard 24wp without having to add such a steep draft angle will be challenging

@AdrianoAguzzi have you tried using these vacuum-formed wells for liquid cultures? could be an interesting way to make custom geometry plates.

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 🧵

Our solution: AutoOpenRaman adds automation to OpenRAMAN while keeping it open-source and relatively inexpensive (~$8k in total). [3/8]

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]

Biological foundation models have hit a plateau. Scaling isn't working as expected. Foundational concepts from evolutionary biology could have predicted this: 🧵 research.arcadiascience.com/pub/idea-phylo… [1/9]

We did something radical that shouldn’t feel radical: we stopped funding science built for journals so that we can reimagine scientific publishing. First at @ArcadiaScience. Now at @AsteraInstitute. More below.

Discovered some unexpected growth phenotypes in Chlamydomonas flagellar mutants! The cpc1-1 strain (with central pair complex defects) shows surprising metabolic traits that might be independent of its flagellar defects. 🧵 research.arcadiascience.com/pub/observatio… [1/9]

We need to grow our team at @ArcadiaScience and just opened a few new roles this afternoon. Join us! jobs.lever.co/arcadiascience

We’re hiring an *evolutionary cell biologist* @ArcadiaScience! This is a hands-on role designing and executing experiments across the tree of life, developing methods for measuring and interpreting phenotypes, and helping us test our tools in vivo! Apply➡️jobs.lever.co/arcadiascience…