Parfois c’est ce qui nous est le plus proche que l’on met le plus de temps à voir. Pendant quinze ans j’ai cartographié les grandes fortunes mondiales, objectivé leurs techniques pour contourner l’impôt dans les paradis fiscaux, du Luxembourg aux îles vierges britanniques... 🧵

Forgetting the gain reference file is why you don't finalize the deposition of a #CryoEM dataset to EMPIAR on a Friday evening... 🤦‍♂️ Good that I have two weeks to fix this.

CryoSPARC now has many fancy algorithms. But the more #CryoEM datasets I process, the more I believe that 3D classification (with no alignment) and local refinement are all we need. Combined with some understanding of the particle under study and carefully crafted masks, they are applicable to […]

Proton Mail Falls Under U.S. Jurisdiction If you read their Terms of Service, at first glance, they reference the laws of Switzerland. However, because they now have offices in the United States — along with registrations, trademarks, copyrights, and patents in the U.S. — they also cite U.S […]

This should have been big news! Ten funding agencies from eight European countries have pledged to support a public infrastructure that is poised to replace academic journals: FWF 🇦🇹 RCN 🇳🇴 Forte 🇸🇪 ARIS 🇸🇮 SRC 🇸🇪 FCT 🇵🇹 CSIC 🇪🇸 DFG 🇩🇪 Formas 🇸🇪 ANR 🇫🇷 Only two of them issued press releases in […]

OMG the newest Coot is on Flathub! 🤩 I wish I had known earlier. https://flathub.org/apps/io.github.pemsley.coot #CryoEM

We're officially in the era of over 100,000 academic journals 🙃 🎉 "After we removed journals with duplicated journal names and International Standard Serial Numbers (ISSNs), 93,804 open-access journals were left" So there's 93,804 OA journals + at least 7,000 non-OA journals Rather than […]

#Sciop hit a Petabyte (actually a Pebibyte but nobody knows that word) of total proven capacity a week or two ago. That's all the seeders * the size of the things they are seeding. All volunteers, zero dollars in funding, piggybacking off existing resources […] [Original post on neuromatch.social]

Last week trump announced plans to "review" 8 Smithsonian museums. Today he doubled down, very explicit about the intent to revise history to reflect the ethno-nationalist fantasy of US history. You can do something about that! We are backing up the digital archives of those museums on sciop […]

An underappreciated difficulty with academic peer-review: removing your name from the PDF metadata of your review report... 😅 I eventually found after some research that Exiftools can do this easily. #academicchatter

I have a #CryoEM screening session booked in a bit more than a week, but after reading the #ccpem list today, I’m scared it will shake the very foundations of physics. 😮 Should I cancel this microscope time? 🤔

please upvote this if you don't mind https://github.com/orgs/community/discussions/169148

@khinsen have you seen this survey on computational reproducibility in HPC: https://ec.europa.eu/eusurvey/runner/computationalReproducibility2025 Thought you might be interested if you hadn't seen it yet.

One thing that the current exorbitant investments in "AI" show is that the investor class and big tech corporations do not pay enough taxes: If you have billions to set on fire for spicy autocomplete we should take some or all of those to do something useful with.

Oh, a new homemade time-resolved vitrification device for #CryoEM ! https://doi.org/10.1101/2025.07.22.666177 Shake-it-up + Back-it-up = Mix-it-up

"Possible End to End to End Encryption: Come Help" @bert_hubert writes: The European Commission is honestly asking for experts to advise them on ways to institute “effective and lawful access to data for law enforcement”. If you are an expert, I urge you to apply to join this group. You have […]

Looks like I accidentally started an #fscfriday on CCPEM... 🤭 😅 #CryoEM #oops

Found another decent use of LLMs: give hexadecimal color codes for colors that you want to tweak, then you can ask what you want in plain language. It is sometimes easier than moving a cursor in a color picker. Too bad it is many orders of magnitude more costly in energy...

Today, every bus in Uppsala was flying two little Swedish flags, as they usually do on public holidays. The French in me thought: how nice that they did this for Bastille Day too! 🇫🇷 As it turns out, today is actually the princess' birthday here. 😅

> On November 28th, 2012, Randall Munroe published an xkcd comic that was a calendar in which the size of each date was proportional to how often each date is referenced by its ordinal name (…) "In months other than September, the 11th is mentioned substantially less often than any other date […]

HN comment on a Typst article: "The definition of insanity is doing the same thing twice and expecting different results. By coincidence, this is the basic way to compile LaTeX."

An interesting use case of LLMs is as a conversational interface to some body of text, as a complement to other forms of navigation: from a table of content or index, via full-text search, or reading specific sections or even the whole text cover-to-cover. Of course the LLM can still make up […]

«The Wikimedia Foundation, the nonprofit organization which hosts and develops Wikipedia, has paused an experiment that showed users AI-generated summaries at the top of articles after an overwhelmingly negative reaction from the Wikipedia editors community.» It's nice to see places where […]

Since I first shared this link on Friday, the amount raised has shot up by more than € 6000, not taking credit for that but well done #fediverse If we get to the €35000 target this week, I promise to post a couple of new #Greenland #science Vids on my @tilvids channel. @icesheets_climate Who […]

Apropos @peertube the french developer collective @Framasoft are currently trying to raise the (for #bigtech derisory) amount of EUR 75,000 to develop the opensource #fediverse competitor app to Youtube. Maybe chuck 'em a few euros if you think it useful? https://support.joinpeertube.org/en/

Today was the last day of a practical course on #CryoEM for PhD students that I helped teaching (first time for me, but this was the 3rd or 4th edition of the course). It was a lot of fun! ❄️ 🔬 🤓 It is an ambitious course. A few lectures about the theory, then mostly practicals all the way […]

When depositing #CryoEM data to #empiar, I can never remember how to determine the "voxel type" requested in the metadate entry form. Over the years, I have asked about it on CCPEM, bookmarked the permalink to the answer I received then (probably in multiple browser profiles) and written similar […]

Just found that there is now a "reactive Python notebook": https://marimo.io @marimo_io Seems inspired by #Plutojl (itself inspired by @observablehq ). This might begin to reconcile me with Python.

I suspect @waldo is secretly trying to reprocess every #CryoEM dataset available on EMPIAR. 🤔

@ct_bergstrom and Jevin T. West have made this excellent resource available called MODERN-DAY ORACLES or BULLSHIT MACHINES? How to thrive in a ChatGPT world https://thebullshitmachines.com/ Text, slides, videos, even short exercises THANK YOU for making this usable for free in educational […]

Handy bilingual mnemonic for tool use. 🪛🔩 #english #spanish #screw #unscrew #tools #mnemonic

Two days to go, 400,000 signatures to find. The Citizens’ Initiative to ban conversion practices now passed the threshold in 7 countries, so we need just any EU citizens at this point. https://eci.ec.europa.eu/043/public/#/screen/home

This story is wild: A rockslide-generated tsunami in a Greenland fjord rang Earth for 9 days https://doi.org/10.1126/science.adm9247 https://www.youtube.com/watch?v=60T9TKuuujs

Specifically the petition to ban conversion therapy practices is lacking enough votes from: - #germany (49.9%) - #sweden (49.96%) - #Netherlands (94%) - #austria (25.5%) - #slovenia (83.14%) - #portugal (24.46%) If you're a citizen of these countries you can help advance a ban on conversion […]

🎉🔬 More news this weekend. @sciety (eLife's preprint evaluation platform) has secured funding from @nlnet to build a Bonfire flavour for federating preprint reviews and discussions. This means federated, community-governed spaces for open discourse around scientific preprints outside […]

I have been approach by an editor of #JOSS (https://fediscience.org/@[email protected]) who told me about #jose (https://jose.theoj.org/ - for which I could not find a Mastodon handle). The idea is to provide a low-hurdle academic reward to provide open access educational material -- with a […]

My own plot of the final orbit, showing the Roskosmos estimate of the path between reentry and impact in purple. I guess that Kosmos-482 SA reentered somewhere along this track between India and the ocean south of Australia.

ESA reports K482SA reentered between 0604 UITC (seen by radar on pass over Europe) and 0732 UTC (not seen by European radars on the next orbit). Roskosmos reports that reentry was at 0624 UTC over the Indian Ocean, but with no details on how they conclude that.

So, everyone worrying about the Venus probe reentry: yes, it's not designed to burn up in the atmosphere, and that's bad. But, remember Starlink? There's something like one Starlink per day reentering now, and they weigh more than the Venus probe! They say they will burn up completely, but now […]

EU's predicted landing possibilities for Kosmos 482 getting smaller "Status 09 May 19:15 CEST ESA’s Space Debris Office currently predicts that the reentry of the descent craft will take place at: 06:37 UTC (08:37 CEST) on 10 May 2025 The uncertainty in this […] [Original post on ai6yr.org]

If your buddy becomes an editor at a Nature journal, your chances of publishing a Nature paper more than double: "For each additional original article published in the two years before the editor’s appointment, these authors had 161% more chances to publish another original article in this […]

Our Glacios in Uppsala got a camera upgrade to Falcon4i/Selectris (from Falcon3, no filter) completed two weeks ago. I used it yesterday for the first time since the upgrade. Got almost 600 exposures per hour without trying very hard to optimize for throughput! 🤩 Mag 0.69 Å/px, total dose 40 […]

At the #ccpem Spring Symposium since yesterday, and it's been so nice! ❄️ 🔬 The schedule is packed and I try to pay attention to the talks, so no live posting. But I'll try to post some of my personal highlights under this post as I find time to reflect. 🧵 Schedule […]

Call for postdoc applications! We are looking for a 1-year postdoc to work on Philosophy of AI here in lovely Umeå. Deadline for applications is May 26th. More information about the fellowship and how to apply can be found here […]

Looking for a #postdoc position? Come work with us on CO2 fixation in #cyanobacteria using #biochemistry and #CryoEM! 🦠 🧪 🧫 ❄️🔬 We are a friendly group. 🙂 https://www.blikstadlab.org/open-positions.html #job #postdoc

Can we publish computational science in a way that makes it explainable, explorable, reviewable, reusable, and citable? Here's a proof-of-concept implementation that suggests the answer is "yes": https://hyperdoc.khinsen.net/ It contains two scientific papers (well, toy examples) and two […]

New blog post: "Why we should review research software" https://blog.khinsen.net/posts/2025/04/11/reviewing-software.html

Framework has stopped selling versions of its base laptop model in the US because of tariffs. Says that if it kept selling them in the US it would lose money. Framework is the only company that makes reliably upgradeable, repairable laptops […]

'Omics has suffered from the imbalance between the great amount of effort that has been put into generated more data and the lack of any significant effort into the more difficult problem of how to use the resulting information effectively.

We’re back: How tuberculosis is set to surge globally once again - Bulletin of the Atomic Scientists https://thebulletin.org/2025/03/were-back-how-tuberculosis-is-set-to-surge-globally-once-again/#post-heading #publichealth #tuberculosis #research