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Cake day: 20 June 2023

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  • The usefulness of alphafold had been grossly overstated by science media. The structures it generates are mostly nonsense, they typically can’t generate molecular dynamics simulation trajectories with the correct physical properties, which makes them not useful for drug discovery. in computational biology today you’ll most often find them in use as a starting point for structure refinement or as one of many sources of data for some integrative method. Again, not useless, and an improvement over previous structure prediction algorithms, but they didn’t ‘solve protein folding’ or anything, like Google might have you believe. I don’t put much stock in Nobel prizes, I mean, they gave one to Henry Kissinger.

    Google also released alphafold 3 under a strict non commercial license, which severely limited its usefulness for both commercial and academic work, the latter of which all but requires using more permissive licenses. I assume Google wanted to monetize a commercial version of it at some point.

    I’ve been using Openfold 3 in some work I’ve been doing recently, and while the software is a bit undercooked, it does produce structures similar to alphafold 3 without any of Google’s bullshit. So I wouldn’t worry too much about this announcement. The protein folding will continue with or without them


  • I have a Shure SM58 on a stand running though a focusrite scarlett and akg k371s. I got the the mic and interface used on eBay. I previously used a behringer xm8500 and a behringer usb audio interface which honestly gets you most of the way there in terms of audio quality. The headphones have a replaceable cable via mini XLR, which is the failure point on most wired headphones.

    I’ve never had audio problems on Linux, these days everything uses a generic driver.






  • I can’t recommend emby because their business practices are pretty scummy. After accepting open source contributions for years, they went closed-source in 2018 and took all those contributions with them (they had a CLA). The very next update, they added hardware acceleration and locked it behind a paywall. They had a pretty big ‘security incident’ a few years ago, which probably would have been averted if they were still open source, as users in the community flagged it as an issue long before the devs took action.



  • WormFood@lemmy.worldtolinuxmemes@lemmy.worldGnome Slander
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    2 months ago

    When Gnome 3 first came out, it was comically unusable, but now a lot of the big issues have been fixed and I find it only mildly idiosyncratic. I like the KDE user experience more but I also think KDE is much buggier. I switched to gnome last year after getting tired of dealing with my desktop freezing/crashing and it’s been pretty smooth sailing. My main complaints are:

    • Switching applications instead of windows on alt-tab (has any computer user ever wanted this?)
    • Modal dialogues have window decorations that inexplicably move the parent window when dragged
    • Typing in Files starts searching instead of navigating to a file/directory with the typed name
    • Opening an archive extracts it automatically instead of looking inside

    The default gnome applications are also quite inferior to their KDE counterparts (Dolphin is leagues ahead of Files, Kate is much better than Gnome’s text editor). But I guess you could install dolphin on gnome if you really wanted, so I won’t hold that against the DE itself.




  • The French revolutionary government had moderate and radical factions that coexisted peacefully for many years. The terror wasn’t something that happened arbitrarily, it was an escalating conflict between radicals and (mostly) counter-revolutionaries acting in the interests the French burgeroise. During the course of the revolution, the government abolished an extremely oppressive system of feudalism, established universal rights for French citizens, established voting rights that would eventually lead to universal suffrage in France, and abolished slavery in the French colonies. That’s not to say it was all good (terror, wars, economic hardship, etc) but it completely transformed the entire country in a matter of years, from feudalism to a limited form of democracy, which resembles our modern democratic states much more closely than the system that had been created during the American Revolution.

    If your take on the French Revolution is ‘they didn’t have a common enemy so they turned on eachother’ then I would say that it’s you who doesn’t know their history very well.



  • I had to use Google to work out how to crop to a rectangular selection on affinity 2. Not sure about affinity 3. I was also really unhappy with the ‘personas’ UI pattern which locks away different photo editing tools into whole parallel universe user interfaces. As a new user it just looked like those features were missing and I had to Google again. It’s not hard to learn but my first impression of the software was googling to work out how to do things that are obvious in any other image editor. Maybe it’s better in affinity 3?



  • A few years ago I replaced Photoshop with Affinity. Affinity’s user interface is pretty awful, even compared to Photoshop, but it does at least run a bit better. A few years ago I switched from premiere pro to da Vinci resolve, and though resolve has a bit of a learning curve, overall I think it’s better than premiere - it’s definitely faster and crashes a lot less.

    I’m hoping that audacity 4 is a good enough audio editor to replace audition - we’ll see, audition is actually pretty good imo but I’d accept a slight downgrade if it means I can get away from Adobe entirely.



  • The UK govt announced £162m in cuts to research council funding last month, then this month they announced £2bn for a massive quantum computing project. I’m all for blue sky research but the field is basically a giant money pit. £2bn would have bought multiple general purpose supercomputers that could have been used for biology, materials science, astrophysics etc. The quantum computing research is inevitably going to yield a quantum processor with less than 1kb of memory that can only run for a few nanoseconds. The government is disproportionately funding this stuff because of the siren song promise that quantum computing will help them break encryption, but the field has taken so long to materialise anything useful that we now have quantum-resistant classical encryption algorithms. Also, plenty of physicists are now skeptical of the idea that quantum computers will be intrinsically faster than classical computers for most tasks.


  • The matrix sequels definitely muddle the pacing and characters, and they struggle to fill the void left by the central mystery of the first film, but the philosophising and action are both as good or better than the first film.

    Speed racer has already been critically reevaluated so I guess my wachowski hot take is that Jupiter Ascending is due. It’s idiotic but it’s a sweaty blast of pure cinema.