Research

Create comprehensive incident reports with knowledge graphs. Use when debugging production issues where you need to trace root cause through multiple code entities. Documents debug process, entity relationships, reasoning→pattern→codebase chain, and prevention strategies.

Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.

--> --- name: scientific-manuscript description: "High-impact scientific manuscript preparation for journals like Nature, Blood, Cell. Use when writing abstracts, introductions, methods, results, discussions, or figure legends. Includes citation management, statistical reporting standards, ICMJE guidelines, and journal-specific formatting for hematology/oncology publications." license: Proprietary ---

Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.

Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.

Analyzes events through psychological lens using cognitive psychology, social psychology, developmental psychology, clinical psychology, and neuroscience. Provides insights on behavior, cognition, emotion, motivation, group dynamics, decision-making biases, mental health, and individual differences. Use when: Behavioral patterns, decision-making, group behavior, mental health, leadership, persuasion, trauma, development. Evaluates: Cognitive processes, emotional responses, motivations, biases...

Query and analyze W&B experiment data and Weave LLM traces using Python scripts. Use when working with Weights & Biases data, including (1) querying ML experiment runs, metrics, and hyperparameters, (2) analyzing LLM traces and evaluations, (3) creating W&B reports, (4) listing projects and entities.

Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

--> --- name: 'pan-cancer-multiomics-agent' description: 'AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Pan-Cancer Multi-Omics Agent** integrates multi-omics data across cancer types to identify shared oncogenic ...

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.

Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint. Use when researching disease targets, finding approved/investigational drugs, searching clinical evidence, discovering genetic associations, or analyzing compound bioactivity data.

Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on topics like segmentation, detection, classification in CT, MRI, X-ray, ultrasound, or pathology imaging. Triggers on requests for "review paper", "survey", "literature review", "综述", "systematic review", or mentions of writing academic reviews on deep learning for medical imaging.

An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning.

Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.

--> --- name: leads-literature-mining description: Review Automator keywords: - literature-mining - systematic-review - meta-analysis - pubmed - evidence-synthesis measurable_outcome: Complete a systematic review screen of 100+ papers with >90% inclusion/exclusion accuracy compared to human baseline. license: CC-BY-4.0 metadata: author: Nature Communications 2025 version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - web_fetch --- A specialized LLM agent fo...

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.

--> --- name: knowledge-synthesis description: Combines search results from multiple sources into coherent, deduplicated answers with source attribution. Handles confidence scoring based on freshness and authority, and summarizes large result sets effectively. keywords: - synthesis - deduplication - summarization - answers - reporting measurable_outcome: Produces a single coherent answer from >5 diverse sources with clear attribution and <10% duplication. allowed-tools: - read_file - run_shel...

Build structured datasets from academic papers. Use when the user wants to extract structured data from scientific literature, traverse citation graphs, search OpenAlex for papers, or create datasets from PDFs for research purposes.

Capture subject matter expertise and domain knowledge that will inform all product decisions - the ubiquitous language, domain rules, and principles from the field

Measure the clinical, utilization, and financial impact of care management programs and population health interventions. Use when evaluating program outcomes, conducting pre/post analyses, comparing intervention cohorts, or reporting program ROI to stakeholders.

Use PROACTIVELY when creating research reports, experiment writeups, technical whitepapers, or empirical study documentation. Orchestrates the complete benchmark report pipeline with structure, diagrams, hi-res PNG capture, and PDF export. Provides working scripts, CSS templates, and complete command sequences for publication-quality AI/ML benchmark reports. Not for slides, blog posts, or simple README files.

Diagnose and audit SEO issues affecting crawlability, indexation, rankings, and organic performance.

Use when experiments complete to judge what claims the results support, what they don't, and what evidence is still missing. Codex MCP evaluates results against intended claims and routes to next action (pivot, supplement, or confirm). Use after experiments finish — before writing the paper or running ablations.