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A personal knowledge base for AI/deep learning papers in biology research. Follows Karpathy's LLM Wiki pattern: Original PDF → LLM markdown summary (sources) → Structured wiki page (wiki).
Language policy: All wiki content is in English. Conversation with Claude can be in Korean or English.
A methodology for using Claude Code + OpenAI Codex CLI to build and maintain a structured, searchable wiki from academic PDFs — designed for researchers who read dozens of papers and want compounding knowledge.
Inspired by Karpathy's LLM Wiki pattern:
Original PDF → LLM markdown summary (sources/) → Structured wiki page (wiki/) → Overview synthesis
| library(rtracklayer) | |
| library(tidyverse) | |
| d <- rtracklayer::import('gencode.v19.annotation.gtf.gz') %>% | |
| as.data.frame() %>% | |
| filter(type == 'transcript') |
| # python 3 | |
| import multiprocessing as mp | |
| from multiprocessing import Pool, cpu_count | |
| number_threads = 8 | |
| ## Creating a pool for parallel processing | |
| pool = mp.Pool(number_threads) | |
| pool.imap_unordered(os.system, cmds ) | |
| pool.close() |
| # terminal color scheme | |
| export PS1="\[\033[36m\]\u\[\033[m\]@\[\033[32m\]\h:\[\033[33;1m\]\w\[\033[m\]\$ " | |
| export CLICOLOR=1 | |
| export LSCOLORS=ExFxBxDxCxegedabagacad | |
| alias ls='ls -GFh' |
| # Get date | |
| date = sapply(strsplit(as.character(Sys.Date()), '-', fixed = T), paste, collapse = "") | |
| ## biomart and AnnotationDbi | |
| # Map a gene id to get an ENTREZ id. | |
| require(AnnotationDbi) | |
| require(org.Mm.eg.db) # mice | |
| entrez = mapIds(org.Mm.eg.db, | |
| keys=ens_gene, # has to be a vector |
| --- | |
| - hosts: <hostname> | |
| remote_user: ec2-user | |
| vars: | |
| s3_spiegel_path: user_s3bucket/path/ | |
| remote_spiegel_dir: data | |
| tasks: | |
| - name: Installing R | |
| yum: name=R state=latest |
| import sys | |
| match = [] | |
| with open(sys.argv[1]) as fh: | |
| for line in fh: | |
| if line in match: | |
| pass | |
| else: | |
| match.append(pass) | |
| // Use Gists to store code you would like to remember later on | |
| console.log(window); // log the "window" object to the console |