CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

Jekyll-based GitHub Pages personal blog “BI Playground” using the Minimal Mistakes remote theme with a custom “Scientific Editorial” design. Content focuses on Bioinformatics, AI, and Drug Discovery. Site language is Korean.

• URL: https://a7420174.github.io
• Title: BI Playground
• Author: 딴생각러 (“개떡이라도 일단 AI한테 던져보기”)
• Branch: master — commits here trigger automatic GitHub Pages deployment (no CI/CD config needed)

Build & Development

# Ruby PATH (Windows)
export PATH="/c/Ruby34-x64/bin:$PATH"

# Install dependencies
bundle install

# Serve locally with live reload
bundle exec jekyll serve
# Site available at http://localhost:4000

# Build without serving
bundle exec jekyll build

Requires Ruby 3.4+ and Bundler. The github-pages gem pins Jekyll and plugin versions to match GitHub Pages.

Note: wdm gem is disabled in Gemfile (incompatible with Ruby 3.4). Windows live reload uses polling instead.

Architecture

• Remote theme: mmistakes/minimal-mistakes — overrides in _includes/, _sass/, _layouts/
• _config.yml: Site metadata, author info, analytics IDs, Utterances comments, plugin list, permalink structure (/:categories/:title/)
• _posts/: Blog posts in YYYY-MM-DD-Title.md format with YAML front matter
• _pages/: Static pages (about with skill cards, custom 404, category/tag/year archives)
• _layouts/home.html: Custom home layout with hero section (DNA base animations) + paginated post list
• _layouts/single.html: Overridden to include Busuanzi page view counter
• _includes/head/custom.html: Google AdSense, custom fonts (Playfair Display, Noto Sans KR, JetBrains Mono), Busuanzi script
• _includes/footer/custom.html: Reading progress bar, back-to-top button, ad-blocker detection banner
• _includes/archive-single.html: Overridden to show teaser images in post list
• _includes/page__meta_custom.html: Busuanzi page view counter display
• _data/navigation.yml: Top nav (Posts, Categories, Tags, About)
• assets/css/main.scss: Comprehensive custom SCSS (~1000 lines) — color palette, typography, hero, post cards, code blocks, 404, skill cards, archive styling

Design System

• Color palette: Teal (#1a6b5a) primary, earth tones, DNA base pair colors (A/T/G/C)
• Typography: Playfair Display (headings), Noto Sans KR (body), JetBrains Mono (code)
• Code blocks: Dark theme (#1e1e2e), rounded corners
• Post cards: White cards with teal accent, hover lift + gradient border
• Hero: Deep teal gradient with floating A/T/G/C DNA base animations

Post Front Matter Convention

title, date, categories, tags, toc (true), toc_sticky (true),
header.teaser, header.og_image

Page defaults in _config.yml auto-apply: layout: single, author_profile: true, read_time: true, comments: true, share: true.

Post Categories & Tags

Current categories: AI, Hail, 채용공고

Common tags: MCP, AI, Bioinformatics, Computational Biology, LLM, scRNA-seq, Scanpy, Automation, Drug Discovery, RSS, Claude Code, AlphaGenome, DeepMind, CELLxGENE, Skill, Tool, 채용, 생명정보학

Key Integrations

• Comments: Utterances (github-light theme, pathname-based issues)
• Analytics: Google Analytics (GTAG: G-2EFXZE61HF), Google/Naver/Bing search console
• AdSense: Auto ads enabled (ca-pub-5246720880132647)
• Search: Google Custom Search Engine + jekyll-algolia plugin
• Pagination: 5 posts per page via jekyll-paginate
• RSS: Atom feed at /feed.xml (jekyll-feed plugin)
• Page views: Busuanzi counter on each post
• Ad-blocker detection: Polite banner in footer

Writing Style

• Korean language with English technical terms (e.g., Chromatin, Pathway, Biomedical, metric)
• Casual, approachable tone — matches “개떡이라도 일단 AI한테 던져보기” vibe
• When citing external data/results, clearly mark whether it’s from official docs or general knowledge
• Always verify image URLs are accessible (200 OK) before using — prefer local /assets/images/ for reliability
• Custom SVG teasers per post stored in /assets/images/

Environment

• API keys: Stored in .env (gitignored) — ALPHAGENOME_API_KEY
• WSL: Ubuntu available for Linux-only packages (e.g., cellxgene-census/tiledbsoma)
• MCP Plugins: Life Sciences marketplace (bioRxiv, PubMed, ChEMBL, ClinicalTrials, Open Targets, etc.)

Scheduled Automation

• Weekly Bioinformatics Job Postings: Remote trigger (trig_01UgCMxFR6oxHoRBqEYbfWA6) runs every Saturday 09:00 KST (cron: 0 0 * * 6 UTC). Collects Bioinformatics & Computational Biology job postings from BRIC BioJob, JobKorea, Saramin, jobs.ac.kr, rndjob.or.kr. Uses Ralph-Loop (Planner→Editor→Validator) role-switching pipeline. Posts to _posts/YYYY-MM-DD-Bioinformatics-채용공고-YYYY년-M월-N주차.md.
  • Excluded sources: Wanted (unreliable deadlines), 하이브레인넷 (403 bot block)
  • Scope: Bioinformatics & Computational Biology only (no wet-lab/general biology)
  • 상시채용: Allowed with (상시) label; concrete deadline postings listed first
  • Manage: https://claude.ai/code/scheduled/trig_01UgCMxFR6oxHoRBqEYbfWA6
• Weekly Bioinformatics News: Remote trigger (trig_014R4st9j2miDXeb54bUaJzx) runs every Saturday 09:00 KST (cron: 0 0 * * 6 UTC). Collects weekly Bioinformatics news: papers (bioRxiv MCP/PubMed MCP), tools (GitHub/Bioconductor/PyPI), conferences (ISMB/RECOMB/ASHG deadlines), industry news (Nature News/GenomeWeb/NIH). Uses parallel subagents (4 collectors) → Editor → Validator pipeline. Posts to _posts/YYYY-MM-DD-Bioinformatics-주간뉴스-YYYY년-M월-N주차.md.
  • Category: Bioinformatics (new)
  • Teaser: /assets/images/weekly-news-teaser.svg
  • Prompt source: _automation/weekly-bioinfo-news-prompt.md
  • Manage: https://claude.ai/code/scheduled/trig_014R4st9j2miDXeb54bUaJzx