Research & Search

holobiomicslab Skill

Use when you have chemical entity records scattered across two or more public repositories (e.g., HMDB, ChEMBL, PubChem, KEGG) and need a single authoritative, deduplicated knowledge base indexed by a queryable identifier (e.g., m/z value or chemical formula).

holobiomicslab Skill

Use when when you have tabulated results (p-value, fold-change, study size N) from two or more independent metabolomics studies addressing the same research question and need a single meta-analytic estimate of effect size and statistical significance without access to raw data or variance estimates.

holobiomicslab Skill

Use when you have (1) peak-picked LC-MS AIF features in a feature table with m/z and retention time, (2) corresponding xcmsSet and RAMClustR pseudo-MS/MS spectral objects from centroid-mode raw data, and (3) a research goal to identify which features are lipids rather than other metabolite classes.

holobiomicslab Skill

Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed and initialized in a coordinated sequence, with explicit dependency declarations and network communication paths between.

holobiomicslab Skill

Use when when building a comprehensive chemical knowledge base for mass spectrometry formula assignment, particularly when you need to link chemical formulae across heterogeneous repositories (HMDB, ChEMBL, PubChem) and connect them through known metabolic transformations to improve annotation.

holobiomicslab Skill

Use when you have CDF-format mass spectrometry imaging files from plant roots with accompanying MATLAB workspace files (.mat), and your research goal is to reproduce linear-axis intensity profiles, feature distributions, and spatial metrics reported in a prior publication (e.g., Sama et al. 2025).

holobiomicslab Skill

Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a peak table, when you need to quantify how many ions passed or failed each filter and summarize the overall filtering impact by status distribution.

holobiomicslab Skill

Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome. Use this skill when your research question requires quantifying local chromatin compartmentalization or annotating structural domain edges for downstream analysis (e.

holobiomicslab Skill

Use when when you have preprocessed metabolomics peak tables (feature matrix with samples × peaks) and sample metadata (phenotype/grouping information and optional continuous covariates), and your research question is to identify which peaks differ significantly between groups while accounting for.

holobiomicslab Skill

Use when when you have CANOPUS chemical class predictions for your samples and need to identify which extracts contain chemical classes absent from the literature for their species or genus.

holobiomicslab Skill

Use when you have a flat table of structure-organism pairs or entity records and need to summarize their distribution across categorical bins (e.g., organism counts binned by number of associated structures in categories: 1, 1–10, 10–100, >100).

holobiomicslab Skill

Use when your research involves searching MS/MS spectra against multiple curated taxonomic or domain-specific databases (microbial, plant, tissue, microbiome, or food origin) and you need to aggregate, compare, and visualize matching results across all domains in a single interface.

holobiomicslab Skill

Use when after applying mpactr's filter suite (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a peak table, use this skill when you need to summarize the overall filtering outcome across all ion categories and present a compact, area-proportional view of which ions passed.

holobiomicslab Skill

Use when when you have a LipidomicsExperiment object with logged and normalized Area measurements, sample grouping metadata (e.g., SampleType, Stage, Race), and a research question about whether specific lipid molecules or classes differ significantly between two or more sample groups.

holobiomicslab Skill

Use when after integrating and curating raw structure-organism pairs from multiple heterogeneous databases, use this skill when you need to verify that each pair and its associated metadata (literature citations, organism taxonomy, chemical identifiers) exist in your authoritative reference.

holobiomicslab Skill

Use when you have identified a claim that one tool outperforms another (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms') in a research article's abstract or introduction, but the specific metrics and results table are not included in the introductory text.

holobiomicslab Skill

Use when when you have two metabolic networks (e.g., from KEGG) and need to measure similarity not by network topology but by the metabolic functions and pathway annotations each organism possesses. Use this skill when your research question focuses on functional overlap—e.

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Astropy workflow skill. Use this skill when the user needs Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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{Feature Name} Research workflow skill. Use this skill when the user needs build and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Astropy workflow skill. Use this skill when the user needs Astropy is the core Python package for astronomy, providing essential functionality for astronomical research and data analysis and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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tavily-web workflow skill. Use this skill when the user needs Web search, content extraction, crawling, and research capabilities using Tavily API. Use when you need to search the web for current information, extracting content from URLs, or crawling websites and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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WellAlly Digital Health Integration workflow skill. Use this skill when the user needs Integrate multiple digital health data sources, connect to WellAlly.tech knowledge base, providing data import and knowledge reference for personal health management systems and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Wiki Changelog workflow skill. Use this skill when the user needs Generate structured changelogs from git history. Use when user asks \"what changed recently\", \"generate a changelog\", \"summarize commits\" or user wants to understand recent development activity and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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XVARY Stock Research Skill workflow skill. Use this skill when the user needs Thesis-driven equity analysis from public SEC EDGAR and market data; /analyze, /score, /compare workflows with bundled Python tools (Claude Code, Cursor, Codex) and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Market Research workflow skill. Use this skill when the user needs Analyze market conditions, geographic opportunities, pricing, consumer behavior, and product validation across Google Maps, Facebook, Instagram, Booking.com, and TripAdvisor and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Scientific Writing workflow skill. Use this skill when the user needs This is the core skill for the deep research and writing tool—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Citation Management workflow skill. Use this skill when the user needs Manage citations systematically throughout the research and writing process and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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PubMed Database workflow skill. Use this skill when the user needs 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 and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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UX/UI Principles workflow skill. Use this skill when the user needs Evaluate interfaces against 168 research-backed UX/UI principles, detect antipatterns, and inject UX context into AI coding sessions and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Gemini Deep Research Skill workflow skill. Use this skill when the user needs Run autonomous research tasks that plan, search, read, and synthesize information into comprehensive reports and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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PubMed Database workflow skill. Use this skill when the user needs 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 and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Scientific Writing workflow skill. Use this skill when the user needs This is the core skill for the deep research and writing tool—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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UX/UI Principles workflow skill. Use this skill when the user needs Evaluate interfaces against 168 research-backed UX/UI principles, detect antipatterns, and inject UX context into AI coding sessions and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

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Claude Scientific Skills workflow skill. Use this skill when the user needs Scientific research and analysis skills and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

thomasmoreai Skill

Verify UK law citations — primarily case law via neutral citation format (UKSC, UKHL, EWCA, EWHC, UKUT) against BAILII, plus UK statutes against legislation.gov.uk — and return verdict JSON.

thomasmoreai Skill

IRAC-scaffolded case analysis memo with research gaps flagged — the scaffold, not the analysis. Rule blocks are RESEARCH NEEDED, Application is STUDENT ANALYSIS prompts, Conclusion is blank. Use when a student needs to scaffold a case analysis memo, write up their analysis, or build an IRAC memo for a case.