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nydame / CLAUDE.md.template_for_bio
Last active July 13, 2026 19:10 — forked from joonan30/AGENTS.md.template
LLM Wiki: AI for Biology -- Collaborator Guide
# LLM Wiki — [YOUR FIELD]
A personal knowledge base of [YOUR FIELD] papers, following [Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/1dd0294ef9567971c1e4348a90d69285):
```
Original PDF → sources/*.md (LLM summary) → wiki/{category}/*.md (final page)
```
**Language policy**: All wiki content is in English. Conversation can be in any language.
@nydame
nydame / llm-wiki.md
Last active July 16, 2026 22:37 — forked from karpathy/llm-wiki.md
llm-wiki

LLM Wiki

A pattern for building personal knowledge bases using LLMs based on Andrej Karpathy's celebrated idea file. I have taken the liberty of drastically editing it down to what is truly essential for my purposes and cost-effective as an LLM input. As such, I also changed POV from that of Karpathy (speaking to me) to my own (addressing an AI agent).

Additionally, I have borrowed from a few other sources:

Upload to your agent and/or put text in CLAUDE.md

@nydame
nydame / GMAIL2json.md
Last active February 13, 2026 22:31
Convert Gmail emails to JSON via EML format

INSTRUCTIONS FOR PROCESSING EMAILS BY LABEL

Export selected emails from Gmail

  • Go to https://takeout.google.com, making sure to log in (or be logged in already) as the owner of the targeted Gmail account.
  • Deselect all, then select only Mail
  • Click "All data included", otherwise you will download the entire mailbox!
  • In the resulting popup, deselect all the annoying default labels and select only the ones you want, e.g. "Project X"
  • Close the pop-up and click "next"
  • Choose
  • file type for compression (.tgz for Mac and Linux)
<?php
function stop_modified_date_update( $new, $old ) {
$new['post_modified'] = $old['post_modified'];
$new['post_modified_gmt'] = $old['post_modified_gmt'];
return $new;
}
add_filter( 'wp_insert_post_data', 'stop_modified_date_update', 10, 2 );
// do stuff that updates post(s) here
@nydame
nydame / viz-diffing.js
Created January 10, 2019 19:37
Visual diffing script
/*
### How to use [Puppeteer](https://github.com/GoogleChrome/puppeteer) for visual diffing
#### Install the following NPM packages: puppeteer, pixemmatch, fs-extra and pngjs (first time only) in the directory where you want to keep your tests
```npm install --save-dev puppeteer pixelmatch fs-extra pngjs```
#### Create your testing script (first time only); what follows is a simplified example that tests only 2 pages
```
*/
const puppeteer = require('puppeteer');
const pixelmatch = require('pixelmatch');
const fs = require('fs-extra');
# Your init script
#
# Atom will evaluate this file each time a new window is opened. It is run
# after packages are loaded/activated and after the previous editor state
# has been restored.
#
# An example hack to log to the console when each text editor is saved.
#
# atom.workspace.observeTextEditors (editor) ->
# editor.onDidSave ->
@nydame
nydame / CookieMaster.js
Last active October 20, 2018 14:34
This JavaScript module lets you store information on the client with localStorage or sessionStorage with a fallback to cookies.
// import CookieMaster
// create an instance, e.g., ```cm = new CookieMaster("localStorage");```
// run ```cm.checkStoreKey(yourKey, yourValue);``` to store your information, providing that the key doesn't already exist
class CookieMaster {
constructor(type) {
// type = "sessionStorage" or "localStorage"; latter is default
this.type = type || "localStorage";
}
@nydame
nydame / conditional-cache-buster.php
Created October 4, 2018 22:28
Conditional cache-busting for WordPress stylesheets
// Tired of making changes to your WordPress site's stylesheet, only to have the client tell you "It looks the same to me!"?
// Force WordPress to send a fresh copy to logged-in users with this simple code snippet.
// (In practice, put this code in your WordPress theme (e.g., in functions.php) or in a custom plugin.)
$now = new DateTime();
$now_version = $now->format('YmdHis');
if (is_user_logged_in()) {
wp_enqueue_style( 'pacificbiosciences-style', get_stylesheet_uri(), array(), $now_version );
} else {
wp_enqueue_style( 'pacificbiosciences-style', get_stylesheet_uri() );
}
@nydame
nydame / Integration of Visual Diffing into Google Puppeteer for Easy End-to-end Testing
Last active August 9, 2020 10:20
How to incorporate PixelMatch into a Node.js script that runs Google Puppeteer
const puppeteer = require('puppeteer');
const pixelmatch = require('pixelmatch');
const fs = require('fs-extra');
const PNG = require('pngjs').PNG;
const testNum = 0; // EDIT before each individual test
const dPath = 'apple.com-20180704'; // EDIT before each set of tests
const filenameBase = 'apple-test';
const pathBase = dPath + testNum + '/' + filenameBase;
(async () => {
[6] pry(#<Post>):1> nesting
Nesting status:
--
0. main (Pry top level)
1. #<Post>
[7] pry(#<Post>):1> self.to_s
=> "#<Post:0x00007fdad6ce57a8>"
[8] pry(#<Post>):1> self.title = "This is a Title Made with Pry"
=> "This is a Title Made with Pry"
[9] pry(#<Post>):1> self.title