Free SKILL.md scraped from GitHub. Clone the repo or copy the file directly into your Claude Code skills directory.
npx versuz@latest install rpazuki-research-workflow-temp-claude-skills-wiki-tocgit clone https://github.com/rpazuki/Research-workflow-temp.gitcp Research-workflow-temp/SKILL.MD ~/.claude/skills/rpazuki-research-workflow-temp-claude-skills-wiki-toc/SKILL.md# SKILL: TOC — Regenerate the Wiki Table of Contents ## Trigger User asks to "update the TOC", "regenerate the table of contents", "refresh the TOC", "rebuild the ToC", or "update index.md". --- ## Purpose `index.md` is a **scientifically organised, human-browsable** table of contents for the wiki. It groups pages by research theme and concept hierarchy — not by folder structure or file type. It is separate from `wiki/index.md`, which is a flat machine-readable catalogue for LLM queries. --- ## Steps ### 1 · Read the current state of the wiki ``` Read wiki/index.md ← full list of all pages and their descriptions Read index.md ← existing ToC to understand current structure ``` Also read `wiki/log.md` (last 50 lines) to understand what has changed since the last ToC update. ### 2 · Identify what is new or changed Compare `wiki/index.md` against the current `index.md`: - Pages present in `index.md` but missing from `toc.md` → must be added - Pages in `toc.md` that no longer exist → remove or mark - New research domains (new top-level topic areas) → may require a new Part ### 3 · Determine correct scientific placement For each new page, decide which section it belongs to based on **scientific meaning**, not folder: | Scientific theme → | Section | |--------------------|---------| | FBA core LP, solution space, underdeterminacy | §1 Mathematical Foundations | | pFBA, dFBA, ecFBA | §2 Core FBA Variants | | FVA, flux sampling, Pareto | §3 Solution Analysis & Uncertainty | | Thermodynamics, enzyme capacity, NED genes, Braess | §4 Constraints Beyond Stoichiometry | | GIMME, iMAT, LBFBA, transcriptomics | §5 Omics Data Integration | | AMN, MINN, FCL, dAMN, hybrid ML | §6 AI/ML-Enhanced FBA | | MICOM, COMETS, syntrophic, community | §7 Community & Multi-Organism Modelling | | MOMA, OptKnock, ALE, strain engineering | §8 Evolutionary Dynamics & Strain Engineering | | COBRA, CHRR, BayFlux (software) | §9 Software & Computational Tools | | E. coli, S. cerevisiae, Y. lipolytica (organisms) | §10 Model Organisms | | Taste prediction, umami, food ML | §11 Taste Prediction & ML | | ESM, ProtBERT, ProtT5, Ankh | §12 Protein Language Models | | Undergraduate topic introductions | Part III Introductory Resources | | Seminar/talk notes | Part IV Talks & Personal Notes | | Analyses | Part V Analyses | | Search records | Part V Searches | **New research domains** (pages that don't fit any existing section): create a new Part or section and note it in the log. ### 4 · Write the updated `index.md` - Keep the existing structure; insert new rows in the correct table - Each row uses **standard Markdown links**, not Obsidian wikilinks: `| [Human-Readable Title](wiki/path/to/file.md) | type | one-line description |` - Path pattern: always `wiki/<subfolder>/<slug>.md` (relative from the repo root) - Use a human-readable title as link text (e.g. `Flux Balance Analysis`, `Orth et al. 2010`), not the raw slug - Use the description from `wiki/index.md` as the basis for the one-liner - If a new section is needed, add it with a brief italicised scope note - Update the `updated:` frontmatter field to today's date - Update the "Last updated" footer line ### 5 · Update `wiki/log.md` Append one entry: ```markdown ## [YYYY-MM-DD] toc | Table of contents regenerated - Added N pages: [[slug1]], [[slug2]], ... - New sections (if any): ... - Removed N stale entries (if any) ``` --- ## What NOT to do - Do **not** include pages outside `wiki/` — the ToC scope is strictly `wiki/**/*.md`. Excluded: - `Notes/Talks/` seminar notes (they live outside the wiki folder) - `raw/` inventory listings from `index.md` - Any other vault files not under `wiki/` - Do **not** mirror the folder structure (`sources/`, `concepts/`, `entities/` — these are file-type groups, not scientific themes) - Do **not** modify `wiki/index.md` — that is maintained by INGEST/SEARCH/etc. - Do **not** delete sections that are temporarily empty; leave them with the scope note only --- ## Output Confirm to the user: - How many new pages were added to the ToC - Which sections were affected - Whether any new sections/parts were created