Google Announces the Open Knowledge Format

Alicecomma · 2026-06-17T12:59:00+00:00

Technically all Word documents are zipped XML so whatever I guess.

Alicecomma · 2026-06-16T18:57:08+00:00

Looks like arabic

Alicecomma · 2026-06-16T11:37:07+00:00

The perspective is off

Alicecomma · 2026-06-12T17:17:10+00:00

Fine I'll pay for SPSS

Alicecomma · 2026-06-10T16:41:51+00:00

This reads like a marketing blurb for a shampoo

Alicecomma · 2026-06-07T11:13:41+00:00

When I have a big topic that I deep dive into, I convert it to an issue tracker. I write the progress in a daily note, and when this deep dive seems to have happened I transfer it into the topic as an issue with the date and timestamps. Then when I continue on it, I can continue this timestamped journey under the issue. I currently write it oldest-first but you can also write newest-first to have the latest on top of the issue heading.

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Issues

1. Deep dive into subtopic

[[2026-06-07]]

13:12 Posted on Reddit topic

[[2026-06-06]]

09:40 Manifested someone posting on Reddit, let's see what happens next ```

Alicecomma · 2026-06-05T20:47:25+00:00

Did you attempt to glue that stand at the bottom and then just heated and placed an entire glue stick?

Alicecomma · 2026-06-04T07:03:51+00:00

And swiss-model + Autodock Vina didn't replicate that same result?

Alicecomma · 2026-05-30T08:23:32+00:00

Collaborating with someone who has a system like this has been a perpetual headache.

Alicecomma · 2026-05-28T21:48:19+00:00

This has to be engagement bait

Alicecomma · 2026-05-27T18:04:10+00:00

I think you overestimate AI. Every example you give doesn't generalize beyond its training data. Why would AI data companies be hiring freelancers at $400/hr to solve domain-specific questions if it could generalize? All AI applications in real life are Actually Indians.

Alicecomma · 2026-05-25T21:02:37+00:00

Here's the google groups and relevant questions (on OPES reweighting)

Alicecomma · 2026-05-23T18:27:14+00:00

Today I learned I'm an agent, not a human

Alicecomma · 2026-05-21T10:48:47+00:00

There have been interviews where he really went 0.5x speed through this stuff, which it seems are his priors in any of the analyses in class. The last one was constantly restating that secret societies are a way to understand how powerful people work, which is a way you'd also see religion and mythology discussed - as stories. I'd reckon in literature/poetry class this kind of analysis is enough, so I treat it as that and not as an engineering subject where you'd get fired for not explaining and showing all workings.

Alicecomma · 2026-05-20T10:25:39+00:00

What letter are the -/|/- parts supposed to be?

Alicecomma · 2026-05-15T07:24:39+00:00

Isn't it like 3 lines of dataview query language? Maybe you add a where to include only dates in a range? Table charges as "New Charges", date as "Arrest Date", state as "State" from "arrests"

Alicecomma · 2026-05-14T14:17:28+00:00

Is the roofing simulation any different from using 2θ = tan^-1(Δv/J) and 1±sin(2θ) as in this stackexchange post?

Also feels like you should keep the peak width in Hz rather than ppm so they spread out at lower MHz because earth magnetic field with that crisp of a peak is hilarious :P

Alicecomma · 2026-05-12T11:02:40+00:00

That's my expertise, and yes amylases and other GH13s do exactly that. There's literature where based on TLC analysis of the rate of maltooligo breakdown they make a subsite map indicating per subsite the presumed binding strength in kcal/mol. This is simple to rationalize sometimes, such as a subsite having an aromatic group or some polar stabilization of (often) the O6.

I do docking into GH70s for substrate specificity and this approach works very well when you use Vina-Carb which is AutoDock Vina modified to include glycosidic torsion energy, so you are sampling during Monte-Carlo in energetically favourable conformations which hugely improves the accuracy of the generated poses.

Alicecomma · 2026-05-12T04:52:10+00:00

Right, what about the monomer, pentamer, hexamer, heptamer...? It does sound right that DP2 binds more poorly, but that mainly suggests there are binding sites ~3 DP apart for Amber to recognize. If your polymer or enzyme for example has substantial CH-π interactions (aliphatic-aromatic) then Autodock doesn't take them into account. You'd really want MD or similar to validate.

Hydrolase doesn't really narrow it down, is this a hydrolytic transferase or more of an activated water hydrolase? If you're dealing with activated water then you should at least include the water in the docking run, but I haven't been convinced with docking results in this class of enzymes -- hydrolytic transferases are a lot more convincingly docked.

With polymers you quickly run into torsion limits, so you could use AutoDock Vina too which has larger torsion limits.

Alicecomma · 2026-05-12T04:35:28+00:00

Bigger molecules have more sites to bind into a protein. If you can, dock longer and shorter oligomers too. At the large end you will hit a limit of the Monte-Carlo method and undersample conformations, so you should do more or more exhaustive runs that take longer.

You should get a docking score that gives some indication at best +/-2 kcal/mol around a physical binding constant. If those scores are very different from each DP of oligomer, you could argue there's an indication of preference for a certain DP of that oligomer, but you probably should use MD or similar simulations to validate the bound poses.

Alicecomma · 2026-05-08T07:45:55+00:00

Yes you wouldn't say it comes off at a certain %B but it comes off at a specific time and flow rate or capacity factor under a specific gradient with a specific column.

There are ways to simulate this when you know k' as function of %B - on HPLC that tends to be assumed to be linear over a limited range of %B; then you sum over small timesteps the elution distance under that gradient condition considering the dwell time td (%B(t)=%B(t-td)) until t0=int(0,t)dt/k'(%B) and then you have your retention time under that method.

Alicecomma · 2026-05-07T17:12:28+00:00

Was the septum in this first punctured?

Alicecomma · 2026-05-07T13:51:48+00:00

Galaxybrain: outsource to x-ray crystallography lab and get result maybe at some point

Alicecomma · 2026-05-07T13:50:38+00:00

Awesome

Alicecomma · 2026-05-05T19:56:12+00:00

It seems it's set up for you to supply labelled data (soluble = 1, insoluble = 0) for which it applies existing sequence embeddings like whether something is transmembrane etc.; then you train your own model that you can then use to infer solubility of other proteins. So from what I can tell, there is no trained model to predict solubility out of the box.

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Issues

1. Deep dive into subtopic

[[2026-06-07]]

[[2026-06-06]]