Alister Burt

elevation profile for a hike 😉

We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!!
www.biorxiv.org/content/10.1...

any technical skills I have today are largely thanks to the incredible mentorship I received through contributions to napari

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

Very cool, awesome to see! 🥳

Very excited to announce that my first, first author paper, is now on BioRxiv! In this paper we unambiguously show #COPII coated vesicles in unperturbed human cells for the very first time!!

Make my day and check it out!
www.biorxiv.org/content/10.1...

#Cryo-ET #TeamTomo #Cryo-CLEM ❄️🔬❄️🔬❄️🔬❄️🔬

Cell tracking is never perfect, and it's important to understand the types of errors your solution contains.

Here is my stab at this: Divisualisations in @napari.org. github.com/bentaculum/d...

You spin tracks out upwards from the playing video. Green edges are correct, FP in magenta, FN in cyan.

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org

If Management is the Only Way Up, We're All F'd - Rand Fishkin
sparktoro.com/blog/if-mana...

Recent tiny blogpost. I mourn Twitter-that-was, and a culture of working in public beyond just the sharing successes and announcements that I see on LinkedIn.

matthewrocklin.com/fail-in-public

(although admittedly this probably is less relevant to the BlueSky crowd)

Matthew Clark holding a tray with a layered rectangular cake, showing the periodic repeating structure of IFT-A and IFT-B. Gingerbread cookies cut in the shape of dynein-2 ride on top.

A close up photo of the cake on a table, showing the periodic repeating structure of IFT-A and IFT-B. Gingerbread cookies cut in the shape of dynein-2 ride on top.

IFT trains are really cool - and what better way to communicate their structure than baking a cake?

Created for my 1st year PhD project with Anthony Roberts and @kattoropova.bsky.social

IFT-A 🟡 IFT-B 🟢 Dynein-2 🔵

I need an AI that will throw the chalk at me if I say something dumb.

Beyond the science the blender renders for figures are awesome, @bradyajohnston.bsky.social would be proud

Happy to share our latest work on the structure and assembly of holocentric kinetochores! Huge thanks to Ines for a very fruitful collaboration, Claudio for all the support, and congratulations to Christine and all co-authors!

www.biorxiv.org/content/10.1...

pay us £1500 for the privilege of doing our graphic design work for free

😂😂😂😂 yes sir!

New cryo-EM lore just dropped ft Niko and lab
#SmallStackHighRes #2DTM #cryoEM
....

For educational purposes only, copyright: 300 (film), Warner Brothers

To tilt or not to tilt? Strategies for in situ cryo-EM data collection Recent breakthroughs in single-particle cryogenic electron microscopy (cryo-EM) and protein structure prediction have transformed our ability to resol…

Check out our recent review discussing the merits of tilt series vs single micrographs for in situ cryo-EM! www.sciencedirect.com/science/arti...

@jeff.cuchazinteractive.org and I wrote a GPU kernel in Mojo for cryo-EM forward projection this weekend as part of the Modular Hack Weekend. On our benchmark volume we generate ~500k projections per second, a ~35x speedup over my PyTorch GPU implementation 🤩

code: github.com/alisterburt/...

Proud to share our latest paper. doi.org/10.1016/j.cr...

Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.

Structural biology in tissue is well and truly here!

@rosfrankinst.bsky.social

teamtomo.org teamtomo.org 🙂

And it’s done! Thanks to everyone who came out for the first edition of FrostByte, our event for the local computational cryo-EMers in the Bay Area ❄️

Special thanks to @joshdcryoem.bsky.social and Ariana Peck for help organizing 🙏

@dtegunov.bsky.social this you?

Michael Sandel: 'The populist backlash has been a revolt against the tyranny of merit' The philosopher believes the liberal left’s pursuit of meritocracy has betrayed the working classes. His new book argues for a politics centred on dignity

“the real problem is not that we have fallen short in trying to live up to the meritocratic ideal, but that the ideal itself is flawed.”

Michael Sandel’s The Tyranny of Merit is worth a read

www.theguardian.com/books/2020/s...

You get it :-) I come at this with a lot less knowledge about systems programming, really appreciate you shining light through some of the cracks

A Pattern Language - Wikipedia

Resonates - from en.wikipedia.org/wiki/A_Patte...

“This is a fundamental view of the world. It says that when you build a thing you cannot merely build that thing in isolation, but must also repair the world around it, and within it, so that the larger world at that one place becomes more coherent, and more whole”

Huh - good to know! You’re right, it’s not where you want it to be in a few key places right now. I guess the question is: will they get there? Your question about I/O seems like it would be important to them, and not supporting hyperthreading goes against their philosophy of maximal hardware util

Will we be able to write interesting parallel programs in Mojo? · modular modular · Discussion #1147 Apologies for the provocative title. I will attempt to define more precisely what is meant by "interesting" parallel programs and what motivates the question. Running pipelines containing nontrivia...

You’re right, it seems missing - this says “can express fully general patterns of parallelism” and “as with most of the Mojo stdlib, the apis for this are not really built out yet, but we'll do that as other higher level language features get built in.”

So… maybe later?🤷‍♂️
github.com/modular/modu...

I seem to have a super high tolerance for this, long form is my favorite 🤪