Blake Riley

88 posts

Blake Riley

Blake Riley

@blake_riley

Proudly Melburnian, fuelled by coffee, dabbling in music & 3D printing. Now in NYC, Postdoc @asrc_gc: allostery in human PTPs w/ #xrays & #xtals. Views my own.

New York City Katılım Şubat 2010
277 Takip Edilen134 Takipçiler
Blake Riley retweetledi
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social@RolandDunbrack·
Demis -- I think AlphaFold3 is really exciting. As Reviewer #3, I got great results from the server. I tried hard to get @Nature to urge you to release the code but was unsuccessful. I did not get it for re-review so I don't know if you responded. So why no code? @GoogleDeepMind
Demis Hassabis@demishassabis

Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. Biology is a complex dynamical system so modeling interactions is crucial blog.google/technology/ai/…

English
25
337
1.6K
675.6K
Blake Riley
Blake Riley@blake_riley·
@DanielKeedy Yep. A foreshock ahead of the big one, when the sun falls out of the sky on Monday?
English
1
0
1
168
Daniel Keedy
Daniel Keedy@DanielKeedy·
Earthquake just now in upper Manhattan... Biggest I've ever felt (and I lived in the Bay Area for 5 years)... Reports of the same thing simultaneously in Queens... Everyone here is safe!...
English
3
0
8
722
Blake Riley
Blake Riley@blake_riley·
Great to see former colleagues @DanielKeedy, Liliana & @DrAliEbrahim connect-the-(diffraction)-dots I left behind in my postdoc! Congrats to LG on her first 1st auth too!
Daniel Keedy@DanielKeedy

New #keedylab #preprint! How does a protein structure differ at physiological temp vs. high pressure (vs. traditional cryo temp)? Liliana Guerrero (Margent) & @DrAliEbrahim looked into it: doi.org/10.1101/2023.0… Great collab w/ Qingqiu Huang & Aaron Finke at @MacCHESSCornell !

English
0
0
5
1.2K
Blake Riley
Blake Riley@blake_riley·
@ingeneousmachin No worries - I got really excited about this too, but looks like for now I'll be hammering work's GPUs. Also thanks for sharing a tracking GitHub issue I can subscribe to!
English
0
0
1
48
Jake Parker
Jake Parker@ingeneousmachin·
Can RFDiffuson be run on Apple silicon? Yes*! I spent a bit of time getting this to work over the weekend, so I thought I'd share. *I've only just started playing with it, so I give no guarantees everything works.
Jake Parker tweet media
English
1
32
182
31.1K
Blake Riley
Blake Riley@blake_riley·
@ingeneousmachin Sure, this change makes the code run, but I think it's on CPU. I think the actual decision on device is in rfdiffusion.inference.model_runners.Sampler.initialize()?
English
1
0
0
132
Jake Parker
Jake Parker@ingeneousmachin·
Now for the code modifications. Just one line in run_inference.py, where you change the device from 'cuda' to ‘mps’.
Jake Parker tweet media
English
2
0
2
1.2K
Blake Riley
Blake Riley@blake_riley·
@ingeneousmachin @YanEVgene Cheers for the instructions Jake! Perhaps a little simpler on this step: I'm just replacing the imports only with `from contextlib import nullcontext as nvtx_range`. Then calls to nvtx_range act as no-ops, without needing to un-indent them.
English
2
0
2
96
Blake Riley
Blake Riley@blake_riley·
I think it's time to admit defeat and declare tab-bankruptcy.
Blake Riley tweet media
English
1
0
3
716
Blake Riley
Blake Riley@blake_riley·
@andrewwhite01 Android here: not really. The Latin characters are all the same width, but whitespace, punctuation is not --- so alignment is not consistent. Those 'other characters' might be halfwidth though?
English
2
0
1
0
Andrew White 🐦‍⬛
Andrew White 🐦‍⬛@andrewwhite01·
Regular: This is a test tweet, to see if monospace works on all device on Twitter 𝙼𝚘𝚗𝚘𝚜𝚙𝚊𝚌𝚎: 𝚃𝚑𝚒𝚜 𝚒𝚜 𝚊 𝚝𝚎𝚜𝚝 𝚝𝚠𝚎𝚎𝚝, 𝚝𝚘 𝚜𝚎𝚎 𝚒𝚏 𝚖𝚘𝚗𝚘𝚜𝚙𝚊𝚌𝚎 𝚠𝚘𝚛𝚔𝚜 𝚘𝚗 𝚊𝚕𝚕 𝚍𝚎𝚟𝚒𝚌𝚎 𝚘𝚗 𝚃𝚠𝚒𝚝𝚝𝚎𝚛 Works?
English
8
0
45
0
Blake Riley
Blake Riley@blake_riley·
@fraser_lab I'm assuming your map transforming is done using matrix_copy? If that's not enough, does "set matrix_mode, 1" help? (Might not, haven't tested it myself). I'm interested, since I have the same sentiment towards chimera syntax.
English
1
0
2
0
Françios Olivier
Françios Olivier@FA_Olivier·
PhD thesis submitted. Please enjoy my "monthly PhD selfie compilation" which started in October 2018. I share this moment with an army of friends, family and colleagues who have contributed to the journey. Thank you.
Françios Olivier tweet mediaFrançios Olivier tweet mediaFrançios Olivier tweet mediaFrançios Olivier tweet media
English
13
1
45
0
Blake Riley retweetledi
Daniel Keedy
Daniel Keedy@DanielKeedy·
The Keedy lab at the @asrc_gc is seeking a computational #postdoc! Lots of exciting project directions linking protein structure, dynamics, allostery, bioinformatics, design, ... We're well funded, & are in a green pocket of NYC. Apply here: rfcuny.org/careers/postin… RTs welcome!
English
1
15
20
0
Blake Riley
Blake Riley@blake_riley·
@GntlmnScientist @lulu_catapano Yeah, that's a frustration for me too. Built-in keybindings and NCS ghosting are dropped (for the moment?), as per the release notes. I'm hoping they come back real soon.
English
1
1
3
0
David Dranow 🇮🇱
David Dranow 🇮🇱@GntlmnScientist·
@lulu_catapano Does the spacebar hit “ok” on the refinement dialog menu? I really miss just hitting space, t, space as I walk through a structure.
English
1
0
5
0
Lucrezia Catapano
Lucrezia Catapano@lulu_catapano·
Coot 1 is out and it’s cooler than ever!🎉 #ccp4 ✅ the GUI has been re-implemented ✅ the graphics has significantly improved, you can now export maps and models as glTF files to be used in #Blender3d and other 3D software. ✅ coot is now a module to be imported in Python 3
Lucrezia Catapano tweet mediaLucrezia Catapano tweet media
English
9
133
537
0
Blake Riley
Blake Riley@blake_riley·
@LucasFarnung @AnaCasanal It's not yet ready for Mac. People involved in the brewsci/homebrew-bio (@brew_sci) community are working on it. When the work is done, it'll be as easy as `brew install coot` 🍻🎉.
English
2
0
7
0
Lucas Farnung
Lucas Farnung@LucasFarnung·
@AnaCasanal Yeah... We need a reward for somebody to come up with a nice homebrew recipe for Mac. Nobody should need a Computer science degree to get Coot installed on a Mac.
English
2
4
16
0
Nicholas McKenzie
Nicholas McKenzie@NJ_McKenzie·
I designed and 3D printed a storage canister with screw top lid for protecting light-sensitive materials in 50mL conical tubes. Foil rips easily imo and this design is reusable and stands up by itself. STL file available here: thingiverse.com/thing:4942006
Nicholas McKenzie tweet mediaNicholas McKenzie tweet media
English
33
199
1.7K
0
Blake Riley retweetledi
Matt Parker
Matt Parker@standupmaths·
If you’ve not had 11:12am in your local time yet today: get ready for the palindrific 2021-11-22-11:12:02 The rest of us can wait for 11 December.
DavinaTheWeena@DavinaTheWeena

@standupmaths Hi Matt, I have a life-long interest in date curios & I've just seen today's ISO date+time palindrome 2021112211202 - I notice the next one is 20211211211202, which if you lop the century & seconds off is 2112112112, ty

English
10
102
680
0
Blake Riley retweetledi
Dr Sheena McGowan
Dr Sheena McGowan@DrSheenaMcGowan·
Are you interested in discovering news ways to combat antimicrobial resistance? We have an exciting opportunity for an early career molecular microbiologist to join our multidisciplinary team. See details here and please feel free to share! careers.pageuppeople.com/513/cw/en/job/…
English
1
38
32
0
Blake Riley
Blake Riley@blake_riley·
@kaczmarski_joe Yeah, this is me. Side chains & cartoon, outlines are great. Surface reps, not so much - I find it more useful to tweak the depth cue and ambient occlusion settings.
English
0
0
1
0
Blake Riley
Blake Riley@blake_riley·
I don't think I've ever seen a more perfect coffee mug! Thanks Eta!
Blake Riley tweet media
English
0
0
7
0

Keşfet

@Nature @GoogleDeepMind @DanielKeedy @DrAliEbrahim @ingeneousmachin @YanEVgene @fraser_lab @stephanie_mul