Research

Use when executed research materials, results, observations, analyses, or draft claims need to become a Research Architect evidence bank, claim register, manuscript-wide display sequence, panel-level evidence map, and bounded interpretation trail.

Use when a Research Architect project has an evidence-ready spine, evidence and claim trail, citation support, terminology/object identities, and display logic that need to become an evidence-first, promise-aware first draft or audited revision.

Use when a Research Architect candidate research spine and approved exemplar adaptation need to become a feasible, field-appropriate study design, analysis plan, validation strategy, and user action plan.

Use when a Research Architect project or existing draft needs claim-level literature support for background, positioning, methods, interpretation, limitations, or revision, rather than broad generic literature searching.

Use when a user needs distinct, feasible Research Architect research-question options from a raw topic, available materials, constraints, and—when available—transferable logic from a target reference paper.

Use when reviewing, revising, or deciding whether to complete a Research Architect draft, especially when its reference adaptation, design, evidence, citations, claim boundaries, copying risk, or missing upstream artifacts need an auditable diagnosis.

Turn a client's Search Console and analytics data into a branded monthly SEO report published as a live, tracked page via ReportRoom. Use when the user says "SEO report for my client", "monthly SEO report", "client SEO report", "SEO deliverable for". Built for consultants and agencies sending recurring monthly reports. For non-SEO client work (status, audits, campaign recaps) use the general client-reporter; for a one-off research share use report-publisher.

Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or compounds, investigating an anomaly, or deciding what experiment or analysis to run next. Triggers on "make discoveries", "explore this data", "find something in", "what's in this dataset...

Throwaway experiments to validate an idea before build.

Karpathy's LLM Wiki: build/query interlinked markdown KB.

Spotify: play, search, queue, manage playlists and devices.

Public-records OSINT investigation framework — SEC EDGAR filings, USAspending contracts, Senate lobbying, OFAC sanctions, ICIJ offshore leaks, NYC property records (ACRIS), OpenCorporates registries, CourtListener court records, Wayback Machine archives, Wikipedia + Wikidata, GDELT news monitoring. Entity resolution across sources, cross-link analysis, timing correlation, evidence chains. Python stdlib only.

Inspect `.session/CURRENT.md`, surface the tactical handoff, and restore only an eligible explicit Codex goal. Triggers: `/resume-session`, `resume session`, `continue where I left off`, `pick up where we left off`. Use when a prior session may contain useful intent, but first reject stale, malformed, branch-diverged, commit-diverged, route-invalid, or reference-only checkpoints. Read legacy `.claude/session-data/CURRENT.md` only before `.session/` exists.

Replace a stale macOS desktop widget after its host app or WidgetKit extension changes. Use when the visible widget is cached, missing, or must be removed and added again.

Write, format, and check UMaT (University of Mines and Technology, Tarkwa) theses, dissertations and BSc/MSc/MPhil/PhD project reports in LaTeX, per the official "Format for the Presentation of Theses and Project Reports" (May 2011). Use when scaffolding a new UMaT thesis, writing or editing chapters, fixing title/declaration/abstract front matter, numbering headings, tables, figures or equations, formatting Harvard citations and the reference list, choosing tenses/units/numerals, or auditing...

Use when adding a paper to the library, citing a paper while writing, or scanning a manuscript for citations. Triggers on "add this paper to the library", "summarize this paper for the library", "cite X here", "scan this grant for citations", a DOI or PDF offered for ingestion, or any work inside ~/repos/papers. NOT for reading a paper to understand it without recording it (use paper-reader), sourcing parameters with citations (use researcher), or multi-stage literature reviews (use lit-pm).

Use when reading, summarizing, or discussing one or a few scientific papers — what the authors found, whether it holds up, and what it means biologically. Triggers on "read this paper", "summarize this preprint", "what does this paper say", a pasted DOI/PMID/PDF path. NOT for sourcing quantitative parameters with citations (use researcher), orchestrated multi-stage literature reviews (use lit-pm), or judging an analysis method's biological validity (use biologist-commentator).

Use Zotero Desktop from Codex to enable/probe the local API, search a local Zotero library, list items/collections/tags, export BibTeX, insert citation keys into LaTeX or Markdown drafts, read indexed full text when requested, and import BibTeX/RIS records into Zotero through the connector server. Use when the user mentions Zotero, citations, references.bib, BibTeX export, local Zotero API, localhost:23119, or adding citations from a Zotero library.

Use when Codex is already in the threat-modeling phase of a security scan, the user explicitly invokes $threat-model, or the user explicitly asks to create, update, or persist a repository threat model. Do not use as the primary trigger for full PR, commit, branch, patch, or repository scans.

Research across Notion and synthesize into structured documentation; use when gathering info from multiple Notion sources to produce briefs, comparisons, or reports with citations.

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus, SLIDE-seq, etc.), performs comprehensive biological interpretation including pathway enrichment, cell-cell interaction inference, druggable target identification, immune microenvironment characterization, and multi-modal integration. Prod...

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics resea...

Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS loci, prioritize causal variants, identify credible sets, or link GWAS signals to causal genes.