Alister Burt
Computational Cryo-EM/ET at Genentech
Love people, the outdoors and building stuff
Complexity is the enemy
All opinions my own
- Reposted by Alister Burt[Not loaded yet]
- Reposted by Alister BurtI've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...
- Reposted by Alister BurtFor anyone with current grants under review at #MRC, this is what's happening, according to Research Professional: www.researchprofessionalnews.com/rr-news-uk-r... We are facing a major #UKsciencefundingcrisis but no outcry, no news. As we said in 2010, #ScienceIsVital, we need to do something!
- Reposted by Alister BurtNobel winner and senior scientists slam cuts to UK physics “These cuts are the inevitable consequence of the government’s choices,” Nobel winner Andre Geim tells me www.researchprofessionalnews.com/rr-news-uk-r...
- definitely the coolest microscopy course around
- Reposted by Alister Burtthe key to me is to distinguish veracity (data provenance), quality (accuracy and competence), interest (who should read it), and importance (significance of the findings for the field). We currently conflate these too much in unidimensional indicators like journal brand/JIF
- Reposted by Alister BurtCheck out our new preprint! We uncover the full molecular mechanism of rotavirus membrane penetration and cytosolic escape using cryo-ET, live-cell imaging, and single-molecule assays. (1/3) 🔗 biorxiv.org/content/10.6...
- Reposted by Alister BurtPhilip Glass boycotting the Kennedy Center Philip Glass boycotting the Kennedy Center Philip Glass boycotting the Kennedy Center Philip Glass Philip Glass Philip Glass Philip Glass Philip Glass boycotting the Kennedy Center
- Reposted by Alister Burt
- one of the more fascinating insights from @matthewcobb.bsky.social’s biography of Francis Crick: he was supposed to write an article for a magazine centred on ‘how to liberate mind and body and protect endangered species (including ourselves) from pathogenic industrial civilisation’ in 1978
- Reposted by Alister Burt
"The Party told you to reject the evidence of your eyes and ears. It was their final, most essential command." "And if all others accepted the lie which the Party imposed, if all records told the same tale, then the lie passed into history and became truth" 1984 - Georges Orwell - Reposted by Alister BurtKare 11 local news just read, in full, this statement from Michael and Susan Pretti, the parents of Alex Pretti. "Please get the truth out about our son."
- Reposted by Alister Burt"Today, lawless and masked thugs masquerading as law enforcement officers brutally killed another American citizen on the streets of Minneapolis without justification”
- Reposted by Alister BurtGenuinely think this coverage is worthy of formal complaint – and if the BBC doesn’t take it seriously, it should be escalated to Ofcom. The appearance of caving to the Trump White House, when the BBC is being sued, could be disastrous for public trust.
- lol OpenAI moved their office a few blocks away and now our building are asking for 30% more rent next year
- Reposted by Alister BurtOne of the most powerful party broadcasts I have seen with a clear message and narrative of hope and change, last was 97 in my eyes. Good one @greenparty.org.uk and @zackpolanski.bsky.social
- Reposted by Alister Burt“In the enterprise and public sector, [Linux] has done nothing to crimp Microsoft's tendrils. Which is where the EU most desperately needs it to succeed. And this is not for want of technical prowess, nor interoperability. In fact, there is far too much.”
- Reposted by Alister BurtWe are running the cryo-ET image processing workshop again this year! Come learn everything tomo: STA, segmentation, heterogeneity analysis from @baradlab.com @williamnwan.bsky.social and others! Apply!
- Reposted by Alister Burt7 days of digital black-out in Iran. One week of darkness... Approximately 20,000 innocent, empty-handed protesters got killed!
- @adamltyson.com I want to register some human brain MRIs for a friend and looked at brainglobe: should I be looking at brainglobe or something else? if so, any recs? c.f. brainglobe.info/documentatio...
- Reposted by Alister BurtWe resolved the molecular architecture of a condensate—inside cells. 🤯 By combining in situ cryoET with multiscale simulations, we show how a single point mutation modifies molecular interactions, shifts the condensate’s material properties, and alters its biological function. Preprint 👇
- We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
- Reposted by Alister BurtRandom infuriating thing of the day. PDBfixer can't be ported over to pip because the name 'pdbfixer' is blocked by PyPI admins for reasons that nobody seems to be able to articulate, preventing packages using those fxns from being fully conda-free
- Reposted by Alister BurtNext: In situ structure and localization of V-atpase in a cool c elegans organelles (from Simone Mattei's lab). Nice analysis of a challenging serial liftout sample and a ribosome-guided tomogram refinement approach. www.biorxiv.org/content/10.6...
- more fun figures in modern day science please and thank you
- Reposted by Alister BurtScience social media reaching breaking point post-Twitter 🤣
- “When I worked on user facing stuff (Maps, Gmail, Accounts) I regularly read the public user support forum … • Almost nobody else in engineering did this • It was viewed negatively by managers and promo committees • The products did always have serious bugs that had escaped QA and monitoring”
- quote is from a comment on the article by Mike Hearn plan99.net/~mike/index....
- This particular Tesla, with this particular license plate, is pretty cool
- “Quality software, in my view, looks simple to its users. But achieving that simplicity requires deep understanding—the user’s workflows, capabilities, background knowledge, essentially everything about them and how our software fits into their lives.” dima.day/blog/build-s...
- (for much of the software I have contributed to I have had little control over the way it looks to users)
- “Propaganda doesn’t shout at you until you believe, it talks at you until you’re too tired to care” youtu.be/BY9uuxC_YAQ?...
- Reposted by Alister BurtCultivate honorable relationships (Adrienne Rich), resist absentminded busyness (Kierkegaard), tell the world how to treat you (Baldwin), embrace enoughness (Vonnegut), and other worthy resolutions borrowed from worthy humans www.themarginalian.org/2016/01/04/r...
- Reposted by Alister Burt"Our very life here depends directly on continuous acts of beginning." A spell against stagnation – John O'Donohue on beginnings www.themarginalian.org/2023/12/30/j...
- Reposted by Alister BurtReally excellent work by the bluesky-less Marie and Sara +coauthors in our lab @embl.org! Check it out for cool combinations of light microscopy and #cryoET, and if you're interested in how yeasts reorganize structurally in response to stressors. #teamtomo
- Structural reorganization underlying stress-induced cytoplasmicsolidification in yeast biorxiv.org/content/10.64898/20…
- Feeling hopeless as the year comes to a close Indifference in the face of tyranny will our downfall
- “then they came for science, and I did not care because I was not a scientist” comes to mind…
- Reposted by Alister BurtMy quote of the day When you're drowning, you don't say 'I would be incredibly pleased if someone would have the foresight to notice me drowning and come and help me,' you just scream. John Lennon
- Reposted by Alister BurtImagine it being easier to just pay the 8 billion dollars and it won't affect you in the slightest. Man what have we done lol
- Reposted by Alister BurtImproving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images [new] Cryo-EM optimization via Sliced Wasserstein: wider basins, robust gradients.
- Reposted by Alister Burtanother robot highlight for 2025: man wearing humanoid mocap suit kicks himself in the balls
- Reposted by Alister BurtA super detailed protocol + video on Cryo-ExM - Cryo-Expansion Microscopy, led by the labs of our former postdocs @marinelap.bsky.social & @ebertiaux.bsky.social. Clear, practical, and very useful for anyone doing nanoscale imaging 🚀 app.jove.com/t/68595/expa...
- Playing Mary had a little lamb with the we will rock you bassline: mind bending
- Reposted by Alister BurtI wrote a bit about practical considerations for using #cryo-ET labels and some things to work on if we want to find any protein in any cell. authors.elsevier.com/a/1mA6h,LqAr...
- Reposted by Alister Burt0.00003 foot tall xmas tree from a Drosophila flight steering muscle 🎄 image by @anne-sustar.bsky.social
- Reposted by Alister BurtJust found these in the basement. made when I was an undergrad #bacteriophages are the coolest! Also note that the duck is laying an egg (I think?). Questionable.
- ☹️
- Reposted by Alister BurtAfter months of hard work learning a new programming language (it's Mojo) and porting some already-optimized C++ code to it, it feels amazing to finally get that big payoff where the new code is 6 times faster! 😀
- Reposted by Alister BurtFinal version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social Huge collaborative effort! So glad to see the community already using it to develop new resources & tools. Check it out here: shorturl.at/z4i4c #CryoEM #CryoET
- Reposted by Alister BurtWe are thrilled to share our new pre-print on the molecular anatomy of nuclear proteasome in human sperm cells! #In-cellcryo-ET + #SPA + #LM! @piotrkolata.bsky.social @a-dsantos.bsky.social, @tomdendooven.bsky.social!! doi.org/10.64898/202...
- Reposted by Alister BurtDon't get me wrong: the original IsoNet was the coolest thing to happen in cryoET in at least a decade. But after the initial “wow” moment it's time to make this topic more sciency
- pretty unambiguous experience in the replies - something is up!
- Reposted by Alister BurtI agree, especially for targets that require global searches. The movement/translation of particles does not work proper if the initial alignments are not good
- Reposted by Alister BurtIf it’s not apoferritin or ribosome, I need to use subTOM to get the initial alignments, then move back to relion. Relion seems to not work well for me for membrane proteins that are relatively small, say EGFR dimer (150kDa total). Once the positions are roughly correct, then it can do a better job!
- Reposted by Alister BurtI noticed something similar, especially with membrane proteins. Dynamo worked fine, but I always got strange reconstructions with RELION.
- Reposted by Alister BurtI currently still use 3D warp subtomos in Relion3 because either version of 2D input data (pseudosubtomos or 2D stacks) give considerably worse results in Relion5 (tested for small particles).
- RELION 5 3D refinement on tomo data often seems to struggle to align objects that old school STA packages handled no problem... does this match everyones experience or is this a me problem?
- a cure is always 5 years away but this looks pretty legit! journal article: www.jci.org/articles/vie... pop sci: med.stanford.edu/news/all-new...
