mycelium

ALWAYS invoke this skill when a user wants to perform computational analysis on data in this repository. This skill loads project-specific analysis conventions, dataset registries, and methodology requirements (validation checks, sensitivity sweeps, null hypothesis testing) that are not available from general knowledge — you cannot do the analysis correctly without consulting it first. Trigger for: running any named analysis technique (clustering, PCA, UMAP, differential expression, survival analysis, dose-response, model fitting, time-series, batch correction, statistical tests), exploring or investigating patterns in data, continuing or extending a previous analysis, debugging or troubleshooting analytical results (wrong clusters, unexpected patterns, parameter tuning). The user's intent must be to computationally process or model data — not just read it, not just look at a file. Do NOT trigger for: reading or previewing data files without analysis, writing reports or documents, brainstorming ideas, setting up or initializing repositories, installing conventions, ingesting or importing data files, fixing code bugs unrelated to analytical results, or updating documentation.

ALWAYS use this skill when the user mentions "mycelium", "living repo", "crystallize", or "todo idea". ALWAYS use for requests about making projects self-documenting, tracking knowledge/decisions/learnings, capturing insights for later, transferring knowledge across projects, or exploring unfamiliar data. This skill manages a .living/ directory framework that registers analyses, datasets, and decisions. It handles: project initialization ("set up mycelium", "initialize living repo"), knowledge capture ("crystallize this learning", "record this finding"), future work tracking ("add a todo idea", "track this for later"), knowledge transfer ("transfer knowledge", "cross-pollinate", "sync learnings"), dataset ingestion, convention installation, and progressive disclosure knowledge systems. NOT for: report writing, code refactoring, brainstorming, git init, or generic folder organization.

Invoke this skill for ANY request involving brainstorming, ideation, or generating new research ideas. This is the brainstorming and idea generation skill. Use it when the user wants to brainstorm, generate ideas, get fresh perspectives, hear what experts from different fields would think, find creative angles they're missing, explore new analysis directions, or get unstuck. Trigger phrases include: "brainstorm", "ideas", "fresh perspectives", "what would a [expert] think", "I'm stuck", "creative angles", "wild ideas", "what are we missing", "open to ideas", "before we write it up", "persona brainstorm", "new directions", "where to go next". If the user's request is open-ended and exploratory rather than a specific concrete task, use this skill. Do NOT use for defined tasks like running a specific analysis, fixing code, setting up projects, or ingesting data.

Use this skill when the user wants to add, import, or ingest files or data into the project. Trigger whenever someone mentions: adding data/files to the project, ingesting a dataset, importing new data, bringing in files from any source, having received results or files from collaborators or facilities, needing to place files into the data directory, or setting up/initializing mycelium. Covers all file types (CSV, FASTQ, XLSX, TIFF, JSON, FCS, TSV, images, etc.). This skill copies/moves files into the project structure, generates metadata, updates the data manifest, and documents provenance. Do NOT use for: reading or analyzing existing project data, listing datasets, deleting data, downloading from URLs, or editing code files.

ALWAYS invoke this skill when a user wants to produce a written document from analysis results in this repository. This skill loads project-specific report templates, section-by-section writing guidance, provenance records, and a QC checklist that are not available from general knowledge — you cannot write a proper report without consulting it first. Trigger for: creating reports, writeups, PDFs, or summary documents from completed analyses; drafting methods or results sections for papers or manuscripts; producing any document artifact the user wants to share, send, or hand off to someone (PI, collaborator, team). The user's intent must be to create a downloadable/sharable document — not to get a verbal explanation. Do NOT trigger for: answering questions about results conversationally, explaining or interpreting findings in chat, creating standalone charts or figures without a surrounding document, performing the analysis itself, ingesting data, setting up repositories, or brainstorming.