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Reposted by Seemay Chou

Diffuse Project @diffuseproject.bsky.social · Aug 14

Want to get involved, share your ideas, or just stay in the loop with email updates? Let us know here: forms.gle/37pK2smABwbg...

Diffuse Project Interest Form

Interested in the Diffuse Project? Please provide your information to help us shape community engagement and potentially direct you to the right project member.

forms.gle

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Seemay Chou @seemaychou.bsky.social · Aug 13

A note in here for other science philanthropists… we have a chance rn to help scientists rethink systems, technical & operational. They’re game to take useful risks, let’s help them. Coming soon: more open science research, experimenting outside journals… seemay.substack.com/p/from-syste...

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Seemay Chou @seemaychou.bsky.social · Aug 12

It will certainly be important to include more modalities (and scientists) beyond X-ray, which we hope to do in the future! Lots of fun work to be done to ensure interoperability in that way

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Seemay Chou @seemaychou.bsky.social · Aug 12

Haha I love that, thanks for actually clicking the link 😂

Reposted by Seemay Chou

Stephanie Wankowicz @stephanieaw.bsky.social · Aug 12

We are thrilled to be part of Project Diffuse, building infrastructure for the dynamic future of structural biology.

We are helping to lead the modeling and encoding efforts of this project, including designing infrastructure that allows AI to learn from the full complexity of experimental data.

Seemay Chou @seemaychou.bsky.social · Aug 12

What’s the next PDB? Maybe it’s …the PDB.

We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇

www.diffuse.science

The Diffuse Project

www.diffuse.science

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Seemay Chou @seemaychou.bsky.social · Aug 12

Oops fixed! Also here seemay.substack.com/p/from-syste...

From systems operators to systems architects

Going up a level from data generation to think about the data systems we design and embed

seemay.substack.com

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Seemay Chou @seemaychou.bsky.social · Aug 12

More on our reflections here seemay.substack.com/p/from-syste...

From systems operators to systems architects

Going up a level from data generation to think about the data systems we design and embed

seemay.substack.com

Reposted by Seemay Chou

Diffuse Project @diffuseproject.bsky.social · Aug 12

Announcing the Diffuse Project! We're unlocking protein dynamics through diffuse X-ray scattering - the overlooked signal that could revolutionize how we understand protein motion. seemay.substack.com/p/from-syste...

From systems operators to systems architects

Going up a level from data generation to think about the data systems we design and embed

seemay.substack.com

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Seemay Chou @seemaychou.bsky.social · Aug 12

Doing this will require co-iterating across an entire data system, not just refining one part. And we're experimenting with how to share all of this (our real-time thinking, pivots, tools, data) openly and quickly all outside of traditional journals

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Seemay Chou @seemaychou.bsky.social · Aug 12

Tldr, we're focusing on diffuse scattering, which is the messier background signal in X-ray diffraction images. These data are often tossed because they're complex, but this complexity is where so much of the interesting biology sits

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Seemay Chou @seemaychou.bsky.social · Aug 12

Our take: more of the same data won't get us there. We're bringing together top experts across almost every node of the X-ray pipeline to generate the right kind of data to model ensembles of different protein conformations. Think: pictures to movies

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Seemay Chou @seemaychou.bsky.social · Aug 12

We're dreaming about the next frontier in structural biology: protein motion. Understanding how proteins move will be the next big unlock for predicting function

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Seemay Chou @seemaychou.bsky.social · Aug 12

What’s the next PDB? Maybe it’s …the PDB.

We just launched @diffuseproject.bsky.social a structural biology initiative exploring protein motion & rethinking how we generate and use experimental data. Quick 🧵👇

www.diffuse.science

The Diffuse Project

www.diffuse.science

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Seemay Chou @seemaychou.bsky.social · Aug 5

Most importantly, first in our new series of organismal spotlight shorts (open source illustrations coming soon!). Sea squirts! www.youtube.com/watch?v=-E9T...

Meet Ciona intestinalis

YouTube video by Arcadia Science

www.youtube.com

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Seemay Chou @seemaychou.bsky.social · Aug 5

Wrote up a post summarizing some of our big picture lessons on bottlenecks, such as difficulties in finding tacit "folklore" knowledge in organismal systems arcadiascience.substack.com/p/zoogle-sug...

It’s true that no model is perfect, but how can we find ones that are less wrong? We’re excited to announce two research partnerships investigating predicted matches between diseases and research orga...

arcadiascience.substack.com

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Seemay Chou @seemaychou.bsky.social · Aug 5

Hoped others would jump on it, but wasn't super straightforward so we ran with some predictions ourselves. Ultimately collaborating with sea squirt and choano experts to scope some pilots (biggest filter was finding people willing to publish openly/rapidly but we prevailed!)

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Seemay Chou @seemaychou.bsky.social · Aug 5

We recently released the Zoogle dataset, which uses our workflows and publicly avail data to quantify how well different organisms model specific human genes/diseases. zoogle.arcadiascience.com/about

Zoogle | Arcadia Organism Selection Portal

Search for the best predicted organismal models for human genes.

zoogle.arcadiascience.com

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Seemay Chou @seemaychou.bsky.social · Aug 5

After many yrs building internally @arcadiascience.com 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 don't miss out on our first organismal spotlight animation featuring sea squirts -- just skip to the bottom! 🧵

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Seemay Chou @seemaychou.bsky.social · Jun 5

Props to those taking the first steps. Those first steps are scary, messy, and the only guarantees I can offer is that now we have a chance at something better. More announcements in coming months.

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Seemay Chou @seemaychou.bsky.social · Jun 5

In the last 48h since announcing our policy, 4 academic PIs decided that they can indeed take this risk w us. They aren't the glam journal "elite" but they're damn good scientists. They're on the more junior side, and that's fucking awesome because they're our future.

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Seemay Chou @seemaychou.bsky.social · Jun 5

#2 is actually a made-up concern in at least 50% of the cases that I help people work through. When you start talking to the real people involved, students are often hungry to try a different way but don't think their PIs will "let" them.

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Seemay Chou @seemaychou.bsky.social · Jun 5

#1 makes sense because they actually think they have the most to lose since their success was built on the existing system. Why would they give up a winning hand even if it's in a broken game?

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Seemay Chou @seemaychou.bsky.social · Jun 5

The "elite" scientists who publish in glam journals are actually waiting for the rest of you. When I talk to them, they either say: 1) Happy to do it once others do, and/or, 2) I can't do it because I have to protect so many trainees.

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Seemay Chou @seemaychou.bsky.social · Jun 5

A v common suggestion I get re: publishing work outside journals is "if you just get some elite scientists to do it, everyone else will do it." This is an instinct that may seem sound, but here's what I've found irl:

Seemay Chou @seemaychou.bsky.social · Jun 3

We're excited to take this step, and to talk to other folks who are interested in experimenting. If you have something you're excited to try, reply here -- and we might even fund it. asterainstitute.substack.com/p/scientific...

Scientific Publishing: Enough is Enough

Why we're no longer funding journal publications

asterainstitute.substack.com

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Seemay Chou @seemaychou.bsky.social · Jun 3

I know this is a hard conversation to have, but it's really important that scientists lead it. Particularly at this moment. We might be able to really change things for the better, especially with all the technologies at our fingertips today.

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