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CODE_MAP (Workspace Topology Index)

This map defines the layout, pipeline matrix, and dependency rules of the Bioinformatics Study Group Okayama University (BSGOU) repository.

1. Directory Structure Outline

LabOnoM.github.io/
├── .github/             # GitHub Actions configurations (cron-based updates)
├── .wiki/               # LLM-Wiki containing domain concept definitions and timelines
├── 00.RawData/          # Raw data directory housing the master PIPELINE_REGISTRY.md
├── GSE284271/           # Visium HD nuclei segmentation datasets and output reports
├── _data/               # Jekyll site data models (YAML/JSON rosters)
├── _includes/           # Jekyll HTML fragments (reusable layouts)
├── _layouts/            # Jekyll layout definitions (home, post, page template wrappers)
├── _posts/              # Jekyll blog posts database (YYYY-MM-DD-title.md)
├── _sass/               # Sass stylesheets for styling variables
├── assets/              # Static assets, fonts, icons, search scripts, and manifest configurations
├── css/                 # Compiled/vendor stylesheets (style.css, bootstrap.min.css)
├── fonts/               # Static typography assets
├── img/                 # General website image assets, slider images, and favicons
├── js/                  # Website logic scripts (custom.js theme & swipe mechanics)
├── scripts/             # Main python pipeline scripts (fetch_bsgou_members.py)
├── sources/             # Generated member lists and contribution tables (HTML/Excel)
└── tools/               # Command-line helper utilities and diff validation scripts

2. Directory & Pipeline Matrix

Component Directory Language Role / Purpose Upstream Integration
scripts/ Python Member contribution parsing, ranking calculations (Poisson normalization) Runs on push events in .github/workflows/update_members.yml
css/ / js/ / img/ CSS / Vanilla JS Site layout styling, theme switching (dark/light), sliding carousels, mobile navigation Interacts with index.html elements
GSE284271/ Python / HTML Visium HD Nuclei Segmentation, spatial binning, Scanpy clustering reports Custom Jupyter/Scanpy analytical pipelines
.wiki/ Markdown AROS LLM-Wiki capturing lessons learned, timeline validation, project specs Grounded to /wiki- workflows and system agents
tools/ Bash / JS Local workspace validations, URL assertions, directory tree generators CLI developer utility helpers

3. External Dependencies & Frameworks

  • Jekyll (Static Site Generator): Compiles HTML pages using Liquid templates. Controlled by _config.yml and Gemfile.
  • Python 3: Used in data parsing scripts (fetch_bsgou_members.py) and data analysis.
    • Key Python Packages: requests, openpyxl (member scraper), scipy, numpy, pandas, scanpy, stardist (spatial transcriptomics analysis).
  • Node.js: Runs image path validation and link assertion scripts (tools/assert-url.js).

4. Key Documentation Index

  • SPEC.md: UI styling, layout parameters, theme class names, mobile suppression, and touch gesture variables.
  • AGENTS.md: Codex Agent behavioral rules, testing instructions (jekyll build), and AROS integration policies.
  • PIPELINE_REGISTRY.md: Tracks status and descriptions of all computational pipelines.
  • .wiki/lessons-learned.md: Logs structural engineering rules, conda compiler flags, and workspace fixes.