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 :)

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


  • Otter@lemmy.caOPtoProgramming@programming.devThe Illustrated AlphaFold
    4 days 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?

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


    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.[

  • Otter@lemmy.catoNo Stupid Questions@lemmy.worldSports
    9 days ago

    Great to hear!

    Some of the communities are quiet, but you’ll find that people engage with your posts when you make them. Especially if there are a good number of subscribers for them

    You can also post on !communitypromo@lemmy.ca or !newcommunities@lemmy.world if you’re reviving one, so that others can see

    Finally, if you’re in contact with the mods on Reddit for a particular team, see if they’d be interested in having the Lemmy community be the official off-site space for the subreddit. People that want to talk about the team without ads/tracking/annoying UI can come here for it

  • At some point I think I’m going to write a post about nice behaviour here. I have to think about it some more… And this is a diverse place anyways, other people might like different things.

    I’d read something like that :)

    Sometimes we also don’t think about how we could be doing something better. Another thing that comes to mind, which I sometimes forget, is upvoting the post that you are commenting on. Usually if I’m commenting, I want more people to see and join the discussion, but I forget to upvote before leaving the tab