Browse Skills — Page 293

tool-delivery

wgpsec/AboutSecurity

向已控目标主机投递工具和文件的方法论。当你已经拿到 shell/webshell/RCE，需要把 fscan、frp、chisel、linpeas、mimikatz 等工具传到目标上执行时使用。覆盖 Linux 和 Windows 全平台文件传输手法（wget/curl/certutil/bitsadmin/PowerShell/python/nc/base64/SMB 等），包括为什么应该在目标机器上而非本地执行工具、如何应对无外网出网、如何绕过杀软检测、执行后痕迹清理。任何涉及'把文件传到目标上'、'在目标上执行扫描工具'、'内网工具投递'、'文件落地'的场景都应使用此技能

tool-design

guanyang/antigravity-skills

This skill should be used for the tool-interface layer of an agent system specifically: writing tool descriptions agents can route on, designing tool schemas and response formats, naming conventions, actionable error recovery messages, MCP server design, tool-set consolidation, and deciding when to add or remove an individual tool. Use this when the unit of work is a single tool or a set of tools. Route project-shape, pipeline architecture, and task-model-fit decisions to project-development; route deciding whether to introduce sub-agents to multi-agent-patterns.

tool-design-sprint-brief

product-on-purpose/pm-skills

Pre-sprint brief that locks challenge, sprint questions, team and role assignments, customer recruiting plan, prototype medium, interview format, logistics, and success criteria before Monday of a Design Sprint. Use after the readiness verdict is Go and before Monday begins. Produces a two-page artifact the team and Decider sign off on as the contract for the next five days.

tool-design-sprint-decide-and-storyboard

product-on-purpose/pm-skills

Day 3 (Wednesday) move of a Design Sprint that runs the art museum layout, heat map, speed critique, straw poll, Decider supervote, rumble-vs-all-in-one decision, and the storyboard that drives Thursday's prototype build. The most decision-heavy day of the sprint. Use Wednesday morning and afternoon after Tuesday's sketches are collected and attribution-stripped. Produces the canonical 5-15 step storyboard that becomes the build spec.

tool-design-sprint-map-and-target

product-on-purpose/pm-skills

Day 1 (Monday) move of a Design Sprint that produces the bundled Monday artifact containing long-term goal, sprint questions (3-7 testable risks), customer or system map (5-15 step flow), expert interview notes, HMW (How Might We) cluster board, and the Decider's chosen target moment. Use Day 1 morning and afternoon after the sprint brief is locked. Sets the design target for Tuesday's sketches and Wednesday's storyboard.

tool-design-sprint-prototype-plan

product-on-purpose/pm-skills

Day 4 (Thursday) move of a Design Sprint that produces the planning artifact for the day. Output covers the prototype role plan (Maker, Stitcher, Writer, Asset Collector, Interviewer), prototype brief (what to build, fidelity bar, time allocation per role), canonical Five-Act Interview script (Welcome, Context, Intro, Tasks, Debrief), trial-run checklist, and Friday participant confirmation tracker. The actual prototype build is craft work outside the skill's AI invocation surface. Use Thursday morning after Wednesday's storyboard is signed off.

tool-design-sprint-readiness

product-on-purpose/pm-skills

Pre-sprint diagnostic that determines whether a team should run a Design Sprint now, postpone it, or do prerequisite work first. Produces a Go / Conditional Go / Wait verdict with diagnosis, recommended preconditions, attendee list, customer recruiting plan, and pre-sprint activities. Use when a team is considering starting a Design Sprint and wants a fast yes/no diagnosis before committing five days of team time and customer recruiting cost.

tool-design-sprint-sketch

product-on-purpose/pm-skills

Day 2 (Tuesday) move of a Design Sprint that structures lightning demos and the four-step independent solution sketch protocol (Notes, Ideas, Crazy 8s, Solution Sketch). Each team member produces one solution sketch individually; the skill orchestrates the day but does not author the sketches themselves. Use Tuesday morning after Monday's target moment is locked. Output is the lightning demo board, sketch assignments, and the cohort of independent sketches that become Wednesday's heat-map material.

tool-design-sprint-test-and-score

product-on-purpose/pm-skills

Day 5 (Friday) sprint-closing move of a Design Sprint that produces the bundled Friday artifact covering per-customer interview observations, best quotes, scorecard grid (sprint questions by customers), observed patterns, hot takes from each team member, and the Decider summary (build, iterate, pivot, or stop, plus highest-confidence learning, most important revision, and next artifact). Use Friday after Thursday's prototype passes trial run and during/after the 5 customer interviews. The sprint's payoff artifact.

tool-design-v2

diegosouzapw/awesome-omni-skills

Tool Design for Agents workflow skill. Use this skill when the user needs Build tools that agents can use effectively, including architectural reduction patterns. Use when creating new tools for agent systems, debugging tool-related failures or misuse, or optimizing existing tool sets for better agent performance and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

tool-evaluation

elophanto/EloPhanto

Evaluate, test, and recommend tools and platforms with weighted scoring, TCO analysis, and strategic adoption planning. Adapted from msitarzewski/agency-agents.

tool-foundation-sprint-approach-options

product-on-purpose/pm-skills

Day 2 morning move of a Foundation Sprint. Forces generation of 3 to 7 candidate approaches as one-page summaries before the team converges on a top bet. Use after Day 1 is signed and before Magic Lenses on Day 2 afternoon. Enforces a minimum of 3 approaches to prevent first-idea anchoring. Each approach summary names what it is, why it serves the differentiators, and includes a simple visual.

tool-foundation-sprint-basics

product-on-purpose/pm-skills

Day 1 morning move of a Foundation Sprint. Forces explicit team choices on target customer, important problem, team advantage, and competitors and alternatives. Produces a single coherent strategic frame that becomes the input to Day 1 afternoon Differentiation. Use after the sprint brief is signed and Day 1 morning is scheduled. Bundled artifact, not four separate decisions.

tool-foundation-sprint-brief

product-on-purpose/pm-skills

Pre-sprint brief that locks scope, the decision the sprint must unlock, team and role assignments, logistics, inputs to bring, and success criteria before Day 1 of a Foundation Sprint. Use after the readiness verdict is Go and before the sprint begins. Produces a one-page artifact the team and Decider sign off on as the contract for the next two days.

tool-foundation-sprint-differentiation

product-on-purpose/pm-skills

Day 1 afternoon move of a Foundation Sprint. Converts the morning's Basics frame into a defensible strategic position by scoring differentiator candidates against customer-perceived value, choosing two committed differentiators, plotting alternatives on a 2x2 chart, writing decision principles, and producing a one-page Mini Manifesto. Use after Basics is signed; before Approach Options the next morning.

tool-foundation-sprint-founding-hypothesis

product-on-purpose/pm-skills

Day 2 end capstone move of a Foundation Sprint. Compresses the sprint's full strategic frame into a single canonical sentence (the Founding Hypothesis) plus an assumption scorecard, why-we-believe, what-could-prove-us-wrong, and recommended next validation step. Use after Magic Lenses is signed. Strict canonical template; paraphrase is not accepted in v0.1.0. The Founding Hypothesis is the spine artifact the sprint exists to produce.

tool-foundation-sprint-magic-lenses

product-on-purpose/pm-skills

Day 2 afternoon move of a Foundation Sprint. Evaluates the candidate approach set through multiple lenses (4 classic plus at least 1 custom) to surface trade-offs, identify consistent winners and contradictions, and produce a top bet plus a backup plan. Use after Approach Options is signed. Lens scoring is a sense-making tool, not mathematical truth; arbitrary precision is a smell.

tool-foundation-sprint-readiness

product-on-purpose/pm-skills

Pre-sprint diagnostic that determines whether a team should run a Foundation Sprint now, postpone it, or do prerequisite work first. Produces a Go / Conditional Go / Wait verdict with diagnosis, recommended preconditions, attendee list, and pre-sprint activities. Use when a team is considering starting a Foundation Sprint and wants a fast yes/no diagnosis before committing two days of facilitated work.

tool-note-and-vote

product-on-purpose/pm-skills

Structured group-decision mechanic that captures silent ideation, voting summaries, and Decider sign-off in a single bundled artifact. Use when a small team needs to make a fast decision with diverse input, when groupthink is a risk, or when a workshop moment demands silent contribution before discussion. Applicable to Foundation Sprint, Design Sprint, and any participatory decision context.

tool-permission-system

simbajigege/book2skills

Design and implement a layered, configurable permission/safety system for agent tools. Use this skill when building an agent that needs to control which tool calls are auto-allowed, which require user confirmation, and which are denied — especially when the system must be configurable across multiple scopes (project/user/enterprise) and extensible via hooks. Triggers on: "权限系统", "工具安全", "tool permission", "permission system", "tool safety", "allow/deny rules", "hook system", "构建安全机制".

tool-probe

microsoft/amplifier-agent

Writes a fixed sentinel to a file to prove the agent invoked this skill through its skills tool in response to a natural-language request. Invoke this skill when asked to run or invoke tool-probe.

tool-routing

openakita/openakita

Decision guide for choosing the right tool when operating websites, browsers, and desktop software. Consult when the task involves web interaction, website automation, or desktop app control.

tool-use-guardian

diegosouzapw/awesome-omni-skills

Tool Use Guardian workflow skill. Use this skill when the user needs FREE \u2014 Intelligent tool-call reliability wrapper. Monitors, retries, fixes, and learns from tool failures. Auto-recovers from truncated JSON, timeouts, rate limits, and mid-chain failures and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

tool-use-guardian-v2

diegosouzapw/awesome-omni-skills

Tool Use Guardian workflow skill. Use this skill when the user needs FREE \u2014 Intelligent tool-call reliability wrapper. Monitors, retries, fixes, and learns from tool failures. Auto-recovers from truncated JSON, timeouts, rate limits, and mid-chain failures and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.

toolbox-talk-generator

datadrivenconstruction/DDC_Skills_for_AI_Agents_in_Construction

Generate safety toolbox talks for construction crews. Create contextual safety briefings based on weather, work activities, and recent incidents. Support multiple languages.

toolify

coreyhaines31/makerskills

When you want to integrate an external tool, API, MCP server, or service into a project — the wizard walks you through auth, config, env vars, client wrapper code, example usage, and an optional smoke test. Scoped to Next.js and Rails projects. Interactive Q&A — starts with the tool name, asks structured questions until the integration is specified, then scaffolds files. Examples — Stripe, Kit, Sanity, Notion, Neon, Supabase, Resend, Postmark, Twilio, Anthropic, OpenAI, Vercel Blob, custom internal APIs. For MCP servers, also handles the .mcp.json wiring. Triggers on "/toolify," "integrate X," "add X to this project," "wire up X," "set up the X integration," "hook up X," "connect X," "add MCP for X." Part of the -ify trifecta (skillify / toolify / loopify). NOT for adding new SKILL.md files — that's skillify. NOT for cron/agent loops — that's loopify.

tooling

dotnet/efcore

Implementation details for the EF Core dotnet-ef CLI and tooling. Use when changing dotnet-ef commands, the ef wrapper, EFCore.Tools (PMC), or EFCore.Tasks MSBuild integration.

tooljet

TerminalSkills/skills

>-

toolkit-evolution

notque/vexjoy-agent

Closed-loop toolkit self-improvement: discover gaps, diagnose, propose, critique, build, test, evolve.

toolkit-skill-author

monte-carlo-data/mc-agent-toolkit

Authors or extends a skill in mc-agent-toolkit. Gates for forbidden buckets and name collisions, applies CONTRIBUTING's extend-or-split rules, then edits a peer skill or hands off to Anthropic's skill-creator and walks the registration checklist.

tools

first-fluke/fullstack-starter

Manage MCP tools with natural language commands — list, enable,

tools-page-generator

kostja94/marketing-skills

When the user wants to create, optimize, or audit free tools pages. Also use when the user mentions "free tools," "tools page," "toolkit," "free [X] tool," "free [X] calculator," "free [X] checker," "lead magnet tool," "programmatic tools," or "tools hub." For content strategy, use content-strategy.

tools-ui

inferen-sh/superpowers

Tool lifecycle UI components for React/Next.js from ui.inference.sh. Display tool calls: pending, progress, approval required, results. Capabilities: tool status, progress indicators, approval flows, results display. Use for: showing agent tool calls, human-in-the-loop approvals, tool output. Triggers: tool ui, tool calls, tool status, tool approval, tool results, agent tools, mcp tools ui, function calling ui, tool lifecycle, tool pending

tooluniverse

mims-harvard/ToolUniverse

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{\"data_folder\":\"<path>\",\"search\":\"<keyword>\"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.

tooluniverse-[domain-name]

mims-harvard/ToolUniverse

[Complete description of what the skill does, which databases it uses, and when to use it. Include specific trigger phrases like "analyze [domain]", "find [data type]", etc. This description is the primary way Claude determines when to use your skill.]

tooluniverse-acmg-variant-classification

mims-harvard/ToolUniverse

Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution, and pathogenicity assessment. Combines ClinVar, gnomAD, computational predictors, and gene-mechanism context.

tooluniverse-admet-prediction

mims-harvard/ToolUniverse

Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, SwissADME drug-likeness, PubChemTox experimental toxicity, ChEMBL clinical data, Lipinski rule-of-five, and CYP interaction data. Use for drug-likeness assessment, BBB penetration, bioavailability, hepatotoxicity prediction, ADME/PK profiling, or screening compound libraries before lab testing.

tooluniverse-adverse-event-detection

mims-harvard/ToolUniverse

Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, regulatory submissions, and detecting rare AE signals not visible in clinical trials.

tooluniverse-adverse-outcome-pathway

mims-harvard/ToolUniverse

Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characterization, and AOP stressor mapping. Distinct from drug-safety analysis (use tooluniverse-pharmacovigilance for drugs).

tooluniverse-aging-senescence

mims-harvard/ToolUniverse

Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease genetics, senolytic-target discovery, and centenarian-genetics queries. Distinguishes correlative vs causal evidence (knockout, intervention).

tooluniverse-antibody-engineering

mims-harvard/ToolUniverse

Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and manufacturing feasibility. Use for biologic-drug optimization, mAb design review, biosimilar engineering, and clinical-precedent comparison.

tooluniverse-antigravity-plugin

mims-harvard/ToolUniverse

Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy), the "agy plugin install <path>" flow, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "the 1000+ scientific tools" / "the harvard tools") working on Antigravity, says the Antigravity plugin or its tools/skills won't load, hits a uvx or MCP-server startup error, asks how Antigravity updates it, wants to pin or remove it, or finds it running an old tool version. Not for the Codex plugin (use tooluniverse-codex-plugin) or Claude Code plugin (use tooluniverse-claude-code-plugin), for running research with the tools, or for authoring new tools or skills.

tooluniverse-binder-discovery

mims-harvard/ToolUniverse

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

tooluniverse-biomedical-fact-lookup

mims-harvard/ToolUniverse

Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to <database>' (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar, ChEMBL, OpenTargets, Reactome, GtoPdb, UniProt...), and multiple-choice biology/medicine knowledge questions where one option must be verified against an authoritative source. NOT for analyzing user-supplied data files (CSV/VCF/h5ad → use the data-analysis router) and NOT for open-ended literature synthesis. Use whenever a single correct answer exists in a public biomedical database and could be looked up rather than guessed.

tooluniverse-cancer-classification

mims-harvard/ToolUniverse

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.

tooluniverse-cancer-genomics-tcga

mims-harvard/ToolUniverse

TCGA/GDC cancer genomics analysis — cohort construction, clinical metadata retrieval, somatic mutation frequencies, survival analysis, and multi-omics integration. Use for TCGA-BRCA-style cohort studies, mutation prevalence by cancer type, survival-by-mutation analysis, and pan-cancer driver discovery. Always cancer-type-specific (don't use pan-cancer counts without cohort context).

tooluniverse-cancer-variant-interpretation

mims-harvard/ToolUniverse

Clinical interpretation of somatic cancer mutations for precision oncology. Transforms a gene + variant + cancer-type input into an actionable report: clinical evidence tier (CIViC, OncoKB), therapeutic options (FDA-approved + investigational), resistance mechanisms, prognosis, and matching clinical trials. Use for tumor-board variant calls, somatic-mutation actionability assessment, and treatment selection. Always cancer-type-specific.

tooluniverse-cell-line-profiling

mims-harvard/ToolUniverse

Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.

tooluniverse-chemical-compound-retrieval

mims-harvard/ToolUniverse

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).

tooluniverse-chemical-safety

mims-harvard/ToolUniverse

Chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, PubChemTox experimental data, GHS/IARC hazard classification, and exposure-context analysis. Use for chemical hazard identification, occupational/consumer-product toxicity, dose-response evaluation, and acute (LD50) vs chronic toxicity assessment. Distinguishes drug toxicity from environmental chemical toxicity.

tooluniverse-chemical-sourcing

mims-harvard/ToolUniverse

Find commercial sources for chemical compounds — PubChem/ChEMBL identity resolution then vendor catalog search across ZINC, Enamine, eMolecules, Mcule. Compares pricing, availability, and identifies purchasable analogs when an exact compound is not in stock. Use for chemical procurement, virtual library curation, and 'where can I buy X' questions for synthesis planning.

tooluniverse-claude-code-plugin

mims-harvard/ToolUniverse

Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ research skills, slash commands, hooks, and the research agent. Use for first-time plugin install, troubleshooting plugin not loading, verifying MCP server connection, listing API key requirements, or configuring auto-update.

tooluniverse-clinical-data-integration

mims-harvard/ToolUniverse

End-to-end drug safety review integrating FDA labels, FAERS adverse event reports, PRR/ROR disproportionality, pharmacogenomic biomarkers, clinical trial data, and published literature. Use for regulatory drug safety reviews, comprehensive pharmacovigilance reports, label-vs-real-world AE comparison, and clinical decision support for drug safety.

tooluniverse-clinical-guidelines

mims-harvard/ToolUniverse

Search and retrieve clinical practice guidelines from 12+ authoritative sources — NICE, WHO, NCCN, AHA, ADA, SIGN, USPSTF, IDSA, NIH consensus, ESMO/ESC/EASL European societies, and US specialty associations. Use for evidence-graded treatment recommendations, dosing protocols, screening guidance, and authoritative-source-prioritized clinical guidance (NICE/WHO ranked above society guidelines).

tooluniverse-clinical-risk-scoring

mims-harvard/ToolUniverse

Compute and interpret validated bedside clinical risk scores and pretest probabilities for an INDIVIDUAL patient — pick the right score for the scenario, gather inputs, run the deterministic calculator tool, and read the result against an interpretation table. Covers CHA2DS2-VASc (AF stroke risk), HAS-BLED (bleeding on anticoagulation), CURB-65 (pneumonia severity / admit decision), qSOFA (sepsis screen), Child-Pugh + MELD-Na (cirrhosis severity / transplant priority), Wells DVT and Wells PE (VTE pretest probability), ASCVD (10-year cardiovascular risk / statin decision), and eGFR CKD-EPI (kidney function / drug dosing). Use when asked things like "stroke risk for this AF patient", "should this patient be anticoagulated", "pneumonia severity — admit or not?", "sepsis screen this patient", "DVT/PE pretest probability", "10-year cardiovascular risk", "cirrhosis severity / MELD score", or "eGFR / kidney function". Pairs CHA2DS2-VASc with HAS-BLED to weigh anticoagulation. NOT for polygenic/genetic risk (use tooluniverse-polygenic-risk-score), NOT for population-level epidemiology/incidence (use tooluniverse-epidemiological-analysis), and NOT for diagnostic test sensitivity/specificity/likelihood-ratio math (use tooluniverse-diagnostic-test-evaluation).

tooluniverse-clinical-trial-design

mims-harvard/ToolUniverse

Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and approval-pathway analysis. Use for trial-protocol design, power/sample-size estimation, comparator selection, and FDA submission strategy. Driven by precedent-based reasoning rather than first-principles math.

tooluniverse-clinical-trial-matching

mims-harvard/ToolUniverse

AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) and clinical state into ranked clinical-trial recommendations with evidence tiers. Searches ClinicalTrials.gov, the EU CTIS register (European/EEA trials), AND the ISRCTN registry (UK/international) plus cross-references CIViC, OpenTargets, ChEMBL, and FDA labels. Use for matching patients to trials by genotype, biomarker-driven trial selection, trial-eligibility scoring, and finding trials across the US, Europe, and the UK.

tooluniverse-codex-plugin

mims-harvard/ToolUniverse

Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on OpenAI Codex. ALWAYS consult this skill for any of those — don't answer from memory, because the exact marketplace name (mims-harvard/ToolUniverse), the "codex plugin marketplace add" then "codex plugin add -m tooluniverse" flow, Codex's startup auto-upgrade behavior, the uvx tooluniverse MCP server, and the API-key env vars are easy to get wrong. Use it whenever someone wants to get ToolUniverse (or "the 1000+ scientific tools" / "the harvard tools") working on Codex, says the Codex plugin or its tools/skills won't load, hits a uvx or MCP-server startup error, asks how Codex updates it, wants to pin or remove it, or finds it running an old tool version — even if they never say the word "plugin". Not for the Claude Code plugin (use tooluniverse-claude-code-plugin), for running research with the tools, or for authoring new tools or skills.

tooluniverse-comparative-genomics

mims-harvard/ToolUniverse

Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries.

tooluniverse-computational-biophysics

mims-harvard/ToolUniverse

Solve quantitative problems in biophysics — pharmacokinetics (PK volume of distribution, clearance, half-life), epidemiology (R0, attack rate), toxicology (LD50, NOAEL), population genetics (Hardy-Weinberg, Fst), enzyme kinetics (Michaelis-Menten), thermodynamics. Use for first-principles quantitative biology calculations, dose calculations, exposure assessment, and biophysical-property estimation.

tooluniverse-crispr-screen-analysis

mims-harvard/ToolUniverse

Analyze CRISPR-Cas9 genetic screens — MAGeCK gene-level scores, sgRNA count QC, replicate correlation, hit prioritization, and pathway GSEA on screen output. Use for genome-wide essentiality screens, synthetic-lethality discovery, dropout vs positive-selection screen analysis, target identification, and resistance-screen interpretation. Includes screen-QC and statistical thresholds.

tooluniverse-cs-setup

mims-harvard/ToolUniverse

Install or update ToolUniverse in Claude Science — create the conda env, install the tooluniverse pip package, and (re)build the tooluniverse-research skill by fetching the current workflow library from GitHub. Use for first-time setup, upgrading the ToolUniverse version, refreshing the bundled workflows after an upstream release, or reinstalling on a new machine.

tooluniverse-custom-tool

mims-harvard/ToolUniverse

Add custom local tools to ToolUniverse alongside the 1000+ built-in tools. Covers JSON-config tools (simplest, no code), Python class tools (REST/SOAP/GraphQL APIs, computational logic), and best-practices for return schemas. Use for wrapping new APIs, adding domain-specific computations, or contributing tools to the registry.

tooluniverse-data-integration-analysis

mims-harvard/ToolUniverse

Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism.

tooluniverse-data-wrangling

mims-harvard/ToolUniverse

Universal data access patterns for downloading and parsing scientific data when ToolUniverse tools don't cover the source, only return metadata, or you need bulk records. Use for VCF/h5ad/BAM/SDF/GCT parsing, multi-step API workflows (search to filter to download to parse), thousands of records at once, or sources with no dedicated tool. Write Python code via Bash for every step.

tooluniverse-dataset-discovery

mims-harvard/ToolUniverse

Find and evaluate research datasets for any scientific question. Maps research questions to required study designs (longitudinal vs cross-sectional, observational vs experimental, single-cohort vs multi-cohort). Use when the user asks 'find data about X', 'where can I get data on Y', or needs a specific cohort/survey/repository. Covers GEO, ArrayExpress, dbGaP, NHANES, UK Biobank, ClinicalTrials.gov, GWAS Catalog, and 30+ scientific repositories.

tooluniverse-diagnostic-test-evaluation

mims-harvard/ToolUniverse

Diagnostic test / biomarker accuracy — sensitivity, specificity, PPV, NPV, likelihood ratios, accuracy from a 2x2 table; ROC curve, AUC, and the optimal cutoff (Youden) for a continuous biomarker; and post-test probability via Bayes. Use when you have test results vs a gold standard (binary 2x2, or a continuous score + true labels) and need to judge how good the test is, pick a threshold, or compute the probability of disease given a result. Emphasizes the prevalence-dependence of PPV/NPV.

tooluniverse-disease-research

mims-harvard/ToolUniverse

Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing candidates), clinical trials, epidemiology (prevalence, incidence), and phenotypes (HPO). Use for full disease overviews, comprehensive disease characterization, and orphan/rare-disease profiling.

tooluniverse-dose-response

mims-harvard/ToolUniverse

Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response data (enzyme/cell assays, drug screening, agonist/antagonist pharmacology). Fits the 4-parameter logistic (Hill sigmoidal) model. Use when you have concentrations + responses and need a potency value, to compare two compounds' potency, or to judge curve quality. NOT for image-derived dose-response (use tooluniverse-image-analysis) and NOT for survival/regression (use tooluniverse-statistical-modeling).

tooluniverse-drug-drug-interaction

mims-harvard/ToolUniverse

Assess drug-drug interactions — CYP metabolic interactions (substrate/inhibitor/inducer), transporter (P-gp, BCRP, OATP) effects, pharmacodynamic synergy/antagonism, clinical significance scoring, and management recommendations. Use for polypharmacy review, prescribing decision support, and safety analysis when adding or switching drugs.

tooluniverse-drug-mechanism-research

mims-harvard/ToolUniverse

Trace drug mechanism of action — primary target → downstream signaling → pathway perturbation → tissue/organ effect → clinical outcome. Uses DrugBank, ChEMBL, KEGG, Reactome, STRING. Use for understanding how a drug works, identifying off-target effects, mechanism-based combination therapy design, and writing mechanism sections of reports.

tooluniverse-drug-regulatory

mims-harvard/ToolUniverse

Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulatory pathway selection. Always specifies the market when reporting status.

tooluniverse-drug-repurposing

mims-harvard/ToolUniverse

Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechanism rationale, clinical-trial precedent, and patent/regulatory feasibility. Use for hypothesis-generating repurposing for orphan diseases, finding existing drugs for new indications, and prioritizing candidates by evidence and feasibility.

tooluniverse-drug-research

mims-harvard/ToolUniverse

Comprehensive drug profiling — mechanism, primary/secondary targets, drug interactions, clinical-trial status, adverse events (FAERS), pharmacogenomics, and approval history. Use for full drug investigation reports, 'tell me about drug X' queries, and assembling drug profiles for clinicians, researchers, or regulatory work.

tooluniverse-drug-synergy

mims-harvard/ToolUniverse

Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-drug and combination effects (inhibition/viability) and need a synergy score. Explains which model to use, what data each one needs, and how to read the score. NOT for looking up pre-computed synergy in a database (use the SYNERGxDB tool / cell-line-profiling skill).

tooluniverse-drug-target-validation

mims-harvard/ToolUniverse

Quantitative drug-target validation pipeline. Scores druggability, selectivity, safety profile, ADMET feasibility, and structural tractability with a composite Target Validation Score (0-100) and GO/NO-GO recommendation. Use for go/no-go decisions on a target before commit-to-medchem, target prioritization across a list, and target-deselection rationale.

tooluniverse-ecology-biodiversity

mims-harvard/ToolUniverse

Ecology, biodiversity, and conservation biology research — species identification (GBIF, NCBI Taxonomy), invasive species impact, ecosystem dynamics, conservation status (IUCN), niche ecology. Use for biodiversity questions, species comparison, invasion biology, conservation prioritization, and ecology-related literature search.

tooluniverse-electron-microscopy

mims-harvard/ToolUniverse

Search and analyze electron microscopy data — cryo-EM density maps (EMDB), fitted atomic models (PDB), raw micrograph datasets (EMPIAR), and cryo-electron tomography volumes (CryoET Data Portal). Use for finding 3D structural data on a protein/complex, comparing experimental EM resolution to AlphaFold confidence, and accessing raw EM data for re-processing.

tooluniverse-enzyme-kinetics

mims-harvard/ToolUniverse

Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki). Fits the MM equation by nonlinear regression (and reports Lineweaver-Burk for reference). Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor. NOT for BRENDA database lookups of published constants (use the BRENDA tools).

tooluniverse-epidemiological-analysis

mims-harvard/ToolUniverse

End-to-end observational epidemiology analysis — from research question (PECO Population/Exposure/Comparator/Outcome) to publication-ready statistical report. Covers cohort/case-control/cross-sectional design, regression with confounders, propensity scoring, sensitivity analysis. Writes Python code for every step. Use for epidemiology study analysis, NHANES/UK-Biobank-style analyses.

tooluniverse-epigenomics

mims-harvard/ToolUniverse

Genomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam computation with ToolUniverse annotation tools. Use for genome-wide epigenomic statistics, methylation analysis, and chromatin-genome integration.

tooluniverse-epigenomics-chromatin

mims-harvard/ToolUniverse

Histone-modification ChIP-seq, ATAC-seq accessibility, chromatin state, and TF binding analysis from ENCODE, Roadmap Epigenomics, ChIP-Atlas. Use for chromatin-state-by-tissue queries, TF-binding-by-region, regulatory landscape mapping, and ENCODE-cCRE annotations. For DNA methylation use tooluniverse-epigenomics; for RNA-seq use tooluniverse-rnaseq-deseq2.

tooluniverse-expression-data-retrieval

mims-harvard/ToolUniverse

Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray datasets by organism/tissue/condition, comparing across studies (case-control, time-series, dose-response), and assessing dataset suitability before downloading. Always uses English search terms.

tooluniverse-fastq-qc

mims-harvard/ToolUniverse

FASTQ quality control and adapter/quality-trimming decisions with local NGS tools — run FastQC on raw reads, summarize a project with MultiQC, interpret per-base sequence quality, per-base N content, adapter content, overrepresented sequences, sequence duplication and GC content, and decide whether (and how) to trim with fastp / Cutadapt before downstream analysis. seqkit for read counts/stats/subsampling. Use when someone asks "run QC on my FASTQs", "are my reads good quality?", "do I need to trim adapters?", "interpret this FastQC report", "what does this WARN/FAIL mean", "why are overrepresented sequences flagged", "should I quality-trim before alignment", "make a MultiQC summary", or "clean up these reads with fastp". NOT for differential expression / DEG analysis (use tooluniverse-rnaseq-deseq2), NOT for read alignment, coverage, or variant calling (use tooluniverse-variant-analysis / tooluniverse-sequence-analysis). Honest: shells out to real local binaries; if a tool is missing it emits an install plan and stops rather than inventing QC numbers, and it never auto-trims or overwrites raw FASTQs.

tooluniverse-functional-genomics-screens

mims-harvard/ToolUniverse

Interpret hits from CRISPR-KO/CRISPRi/shRNA screens by integrating DepMap essentiality, gnomAD constraint scores, pathway context (Reactome, STRING), druggability (DGIdb), and clinical evidence (CIViC, COSMIC). Use for screen-hit prioritization, essentiality ranking, and turning a list of screen hits into a prioritized target shortlist.

tooluniverse-gene-disease-association

mims-harvard/ToolUniverse

Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet. Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak). Use for 'which diseases is gene X associated with' or 'which genes cause disease Y' queries with quantitative confidence.

tooluniverse-gene-enrichment

mims-harvard/ToolUniverse

Gene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA. Use for interpreting DEG lists, screen hit lists, or any gene-list-to-pathways query. Includes simplify-cutoff handling and union-vs-total denominator conventions for percent-DE questions.

tooluniverse-gene-regulatory-networks

mims-harvard/ToolUniverse

Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout/overexpression). Use for 'which TF regulates gene X', 'which genes does TF Y target', regulatory pathway reconstruction. Distinguishes direct (binding) vs indirect (co-expression) regulatory evidence.

tooluniverse-gpcr-structural-pharmacology

mims-harvard/ToolUniverse

GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric vs allosteric pocket characterization.

tooluniverse-gwas-drug-discovery

mims-harvard/ToolUniverse

Transform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable proteins via DGIdb/OpenTargets, then to existing drugs via ChEMBL. Use for GWAS-to-target hypothesis generation, druggable-fraction analysis of disease loci, and human-genetics-validated drug-repurposing prioritization.

tooluniverse-gwas-finemapping

mims-harvard/ToolUniverse

Statistical fine-mapping of GWAS loci using credible sets (SuSiE, FINEMAP) and locus-to-gene scoring (Open Targets L2G). Identifies likely causal variants and target genes — distinct from positional 'nearest gene' which is often wrong. Use for prioritizing causal variants at GWAS hits, comparing fine-mapping methods, and converting lead SNPs to target genes.

tooluniverse-gwas-snp-interpretation

mims-harvard/ToolUniverse

Interpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gnomAD frequency. Use for 'what does this SNP do', SNP-to-mechanism tracing, and resolving lead-SNP-vs-causal-variant ambiguity. Always considers LD structure before claiming a SNP is mechanistically responsible.

tooluniverse-gwas-study-explorer

mims-harvard/ToolUniverse

Compare GWAS studies, perform meta-analyses across cohorts, and assess signal replication. Uses GWAS Catalog metadata, study-level statistics, and cross-cohort comparison. Use for evaluating GWAS reproducibility for a trait, meta-analysis sample size and effect-size aggregation, and detecting study heterogeneity (population, design, ancestry).

tooluniverse-gwas-trait-to-gene

mims-harvard/ToolUniverse

Discover causal genes for diseases/traits from GWAS data using Open Targets L2G (locus-to-gene) scoring — integrates eQTL, chromatin interaction, and distance evidence. Use for trait-to-gene mapping, drug-target hypothesis generation from GWAS, and replacing the 'nearest gene' heuristic with multi-evidence L2G scores.

tooluniverse-hla-immunogenomics

mims-harvard/ToolUniverse

HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer immunotherapy. Uses IMGT (HLA polymorphism), IEDB (epitope-MHC binding), UniProt (annotation), DGIdb (druggability). Use for HLA typing/imputation review, vaccine HLA coverage, and immunotherapy prediction biomarkers (HLA-LOH, neoantigen presentation).

tooluniverse-image-analysis

mims-harvard/ToolUniverse

Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.

tooluniverse-immune-repertoire-analysis

mims-harvard/ToolUniverse

TCR/BCR repertoire analysis — V(D)J segment usage, CDR3 sequence diversity, clonality scoring, antigen specificity matching to IEDB, public-clone identification. Use for adaptive immune response characterization, post-treatment immune monitoring, antigen-specific clone tracking, and clonal-expansion analysis in immunotherapy or vaccination studies.

tooluniverse-immunology

mims-harvard/ToolUniverse

Immunology research workflows: antibody-antigen interactions, T/B cell repertoire, MHC/HLA binding prediction, autoimmune disease genetics, vaccine epitope mapping. Uses IEDB, IMGT, SAbDab, UniProt. Use for adaptive immunity questions, immune response analysis, antibody/TCR/BCR characterization, immunogenicity prediction, and immune-pathway-to-disease mapping.

tooluniverse-immunotherapy-response-prediction

mims-harvard/ToolUniverse

Predict patient response to immune checkpoint inhibitors (ICIs) by integrating tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression, HLA status, and immune-related gene expression. Outputs ICI Response Score with drug-specific recommendations and resistance-risk assessment. Use for melanoma/NSCLC/RCC immunotherapy decision support.

tooluniverse-infectious-disease

mims-harvard/ToolUniverse

Rapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases (ChEMBL, DGIdb), and literature surveillance (PubMed/EuropePMC). Use for emerging-pathogen profiling, antiviral candidate identification, and outbreak intelligence reporting.