Use when performing mathematical physics computations - Lie algebras, quantum chemistry, neural operators, theorem proving, or scientific validation.
Thermodynamics from the zeroth law through statistical mechanics. Covers temperature and thermal equilibrium, heat transfer mechanisms (conduction, convection, radiation), the…
Combined research, decision, and codification workflow. Use when: (1) Exploring a question before committing (2) Making a decision that needs documentation (3) User says — from…
Analysis of Competing Hypotheses. Operationalizes Richards Heuer's CIA-tradition technique for systematically narrowing among multiple hypotheses against evidence.
Produces a clustered theme map that groups many raw notes, observations, quotes, or data points bottom-up into a small set of named, traceable themes (the KJ method).
Abductive reasoning about causes. Takes a phenomenon, separates observations from interpretations, then spawns diagnosticians applying different reasoning lenses (technical,…
Apply Karpathy framing — AI agent 架構 / skill as code / auto-research / 學習工作流 / human-vs-agent split / 教育設計.
Researches a thinking framework end to end and produces a schema-valid proposed registry entry plus a learning dossier, grading the evidence on the seven-tier model and assessing…
First-person rigor patterns for non-trivial work — type/dimension check, decompose, bound-then-refine, sanity at limits, falsifiability.
Use when adding a new policy-heavy specialist agent, when reviewing why an existing agent is making sloppy mid-flight decisions, or when the model is acting on tool output without…
Multi-mode analytical thinking — first principles decomposition, iterative depth analysis, multi-agent council debates, adversarial red teaming, and scientific hypothesis testing.
Apply parsimony principle to prefer simpler explanations with fewer assumptions. Use for hypothesis selection in debugging, architecture decisions, and choosing between competing…
Multi-source research on concepts and ideas. Combines web search, documentation lookup, and codebase analysis into structured findings.
Hypothesis → Prediction → Test → Revise with explicit falsification. Use for debugging, feature experimentation, performance investigation, and A/B testing design.
Test ideas through hypothetical scenarios when empirical testing is impractical. Use for architecture evaluation, edge case analysis, ethics considerations, and strategy…
Use when tackling complex reasoning tasks requiring step-by-step logic, multi-step arithmetic, commonsense reasoning, symbolic manipulation, or problems where simple prompting…
Run a dynamic ThreadOps research workflow for current-doc lookup, technical comparison, architecture options, cross-checked source synthesis, or decision support.
Design a collision and physics layer for a three.js game, including character movement, collision layers, scene queries, and engine-adapter boundaries.
Comprehensive guide for developing MailExtensions for Mozilla Thunderbird, including Manifest V2/V3 configuration, all messenger.* APIs, UI actions, Experiment APIs, and ATN…
Contract-driven ticket execution with Linear integration - orchestrates intake, research, questions, spec, implementation, review, and done phases with explicit human gates
Exhaustive problem space exploration using the MIT Synthetic Neurobiology "tiling tree" method. Partitions a problem into MECE (Mutually Exclusive, Collectively Exhaustive)…
Analyzes time-series data for patterns, trends, seasonality, and anomalies, with forecasting using statistical and machine learning methods.
Plan and control time-step policies for transient simulations — couple CFL and physics-based stability limits with adaptive stepping, ramp initial transients through sharp…
Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.
Fast and accurate code statistics tool written in Rust. Counts lines of code, comments, and blanks across 200+ languages, with output in JSON, YAML, or CBOR for programmatic…
Run coding and research tasks with lower token waste by reducing repeated reads, broad rewrites, unnecessary narration, and avoidable re-analysis.
Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms.
Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting…
Research the gear and tone behind a song or artist. Produces a SongProfile.md with sourced gear breakdown, inventory-matched Applied section, and conversational follow-up — from…
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…
Research-backed CLI tool refresh workflow for updating existing tools with TDD checkpoints and CLI invocation validation.
Unity physics patterns including character controllers, collision handling, and tunneling prevention.
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches.
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs…
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks…
Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it with findings from 10 research…
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections.
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG…
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions.
Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to compare study designs, effect…
Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of…
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3…
Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction.
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases.
Neuroscience research workflows: neuroanatomy, neural circuits, neurotransmitter biology, neurological/psychiatric disease genetics, neural-protein function.
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses…
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance…
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering.
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.
Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering,…
Perform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regression (binary/ordinal/multinomial), mixed-effects models,…
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug…
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions.
Use when planning a topic cluster (hub + spokes) for a new content area. The agent researches the space, identifies the hub topic, maps the spokes, and produces a specific content…
Pre-search topic resolution. Maps vague queries to concrete entities (GitHub orgs, X handles, subreddits, docs URLs) before searching.
Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep lear — from…