Otter

I waddled onto the beach and stole found a computer to use.

🍁⚕️ 💽

Note: I’m moderating a handful of communities in more of a caretaker role. If you want to take one on, send me a message and I’ll share more info :)

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Joined 1 year ago
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Cake day: June 5th, 2023

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  • OtterOPAtoProgramming@programming.devThe Illustrated AlphaFold
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    8 hours ago

    Who should read this

    Do you want to understand exactly how AlphaFold3 works? The architecture is quite complicated and the description in the paper can be overwhelming, so we made a much more friendly (but just as detailed!) visual walkthrough.

    This is mostly written for an ML audience and multiple points assume familiarity with the steps of attention. If you’re rusty, see Jay Alammar’s The Illustrated Transformer for a thorough visual explanation. That post is one of the best explanations of a model architecture at the level of individual matrix operations and also the inspiration for the diagrams and naming.

    There are already many great explanations of the motivation for protein structure prediction, the CASP competition, model failure modes, debates about evaluations, implications for biotech, etc. so we don’t focus on any of that. Instead we explore the how.

    How are these molecules represented in the model and what are all of the operations that convert them into a predicted structure?












  • OtterOPAtoOpensource@programming.devIntroducing PCSX2 2.0
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    19 hours ago

    PCSX2 (a PlayStation 2 emulator for the PC)

    Windows, Linux and MacOS from what I can tell

    Some changes listed:

    GUI

    You might know the name wxWidgets from its time as PCSX2’s choice of GUI, or from other emulators like Dolphin which used it before migrating to Qt. For a long time, it served us sufficiently well, but its age and implementation began to show rather quickly. Threading issues resulted in deadlocks and race conditions, because it was not properly separated from the emulation core. The technical debt started high and only got worse as the project tried to keep moving forward.

    But now, wxWidgets is gone. No more desktop experience reminding you of what Windows desktop apps looked like in 2006. Qt brings with it a slick appearance, more efficient UI backend, and provided the perfect opportunity to redo all our menus and widgets.

    Settings / Config

    But then we had a thought: since we are already shipping a database file with information on games, why not include more information about what settings a game needs to run correctly? And so PCSX2’s new “game index” was made a reality. It contains a complete list of all known games, and with this index, we now ship pre-configured fixes to ensure your games will automatically run smoothly. You no longer need to remember to enable those graphics fixes every time you switch games - PCSX2 will already know what that game needs and do it for you!

    Custom Settings / Config

    PCSX2 now includes per-game settings which are detached from your global settings. The per-game settings will always default to inherit from your global settings, but they allow you to explicitly set a value for one game in particular. Now if you want to run a game at a higher resolution than the rest or use specific memory cards for different games, you can set it once in your per-game settings and forget about it.

    Compatibility:

    Right now, the list of games which aren’t playable has been whittled down to a small handful with servers which have gone offline, highly obscure peripherals that no one has replicated in emulation yet, bizarre FPU math causing games to break themselves, or over-engineered engines which would bring even the best PC hardware to a literal crawl if it were emulated correctly.

    All that remains of the ‘Nothing’ category is a single game which refuses to boot on Windows. Boot a game in PCSX2 besides that one, and it will at least get you into a menu. Provided no one uncovers any more obscure PS2 games that have been lost to time, it is safe to say PCSX2 has entered the final frontier of compatibility. The challenge now is to get the last few games up and running.

    And others I haven’t read through yet



  • Also, we should consume it (or other types of dietary fibre)

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614039/

    Dietary fibre is that part of plant material in the diet which is resistant to enzymatic digestion which includes cellulose, noncellulosic polysaccharides such as hemicellulose, pectic substances, gums, mucilages and a non-carbohydrate component lignin. The diets rich in fibre such as cereals, nuts, fruits and vegetables have a positive effect on health since their consumption has been related to decreased incidence of several diseases. Dietary fibre can be used in various functional foods like bakery, drinks, beverages and meat products. Influence of different processing treatments (like extrusion-cooking, canning, grinding, boiling, frying) alters the physico- chemical properties of dietary fibre and improves their functionality. Dietary fibre can be determined by different methods, mainly by: enzymic gravimetric and enzymic—chemical methods. This paper presents the recent developments in the extraction, applications and functions of dietary fibre in different food products.

    Not that we should go around gnawing on wood like beavers, but maybe that’s why some indigestible foods seem like we should be able to eat it



  • OtterAtoNo Stupid Questions@lemmy.worldWhere does plaque come from?
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    1 day ago

    As a follow-up question of what the composition looks like

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503789/

    The oral cavity has the second largest and diverse microbiota after the gut harboring over 700 species of bacteria. It nurtures numerous microorganisms which include bacteria, fungi, viruses and protozoa. The mouth with its various niches is an exceptionally complex habitat where microbes colonize the hard surfaces of the teeth and the soft tissues of the oral mucosa. In addition to being the initiation point of digestion, the oral microbiome is crucial in maintaining oral as well as systemic health. Because of the ease of sample collection, it has become the most well-studied microbiome till date.

    Oral cavity is one of the most well-studied microbiomes till date with a total of 392 taxa that have at least one reference genome and the total genomes across the oral cavity approaching 1500.[21]

    Approximately 700 species of prokaryotes have been identified in it. These species belong to 185 genera and 12 phyla, of which approximately 54% are officially named, 14% are unnamed (but cultivated) and 32% are known only as uncultivated phylotypes.[9] The 12 phlya are Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Spirochaetes, SR1, Synergistetes, Saccharibacteria (TM7) and Gracilibacteria (GN02).[22] At the genus level, there is a conserved oral microbial community in healthy mouths. Diversity in the microbiome is individual specific and site specific, despite the similarities. The tongue has numerous papillae with few anaerobic sites and hence harbors a diverse microflora which also includes anaerobes. The areas with low microbial diversity are the buccal and palatal mucosae.[






  • OtterOPAtoLemmy.ca's Main CommunityFediverse Canvas 2024 | Canada Discussion Thread
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    2 days ago

    It’s inspired by a game / social experiment Reddit did a few years ago, where every account can only place one pixel every now and then. Over time, people can work together to make different designs.

    Often we had a Canadian flag, and various symbols for different Canadian provinces, schools, or sports teams.

    That’s the idea here, only this one is open to the entire fediverse. I imagine it didn’t get much advertising prior to the launch, and so it’s quieter than the usual activity on the fediverse.

    Right now I think we’re looking for a design template to follow, so that we can work on something more effectively :)