academic-chapter-writer
Comprehensive academic textbook chapter writing system for medical/scientific content. Use when the user wants to: (1) Write a full textbook chapter (5,000-15,000 words) on any medical/scientific topic, (2) Generate a detailed table of contents with section word counts, (3) Research topics via PubMed MCP and compile 20-30 references, (4) Write section-by-section with proper citations in Vancouver format, (5) Create publishable academic content with Eric Topol-inspired voice and authentic human prose, (6) Get approval at TOC stage before writing begins, (7) Export well-structured chapters for textbook publication.
cardiology-science-for-people
Write rigorous, accurate cardiology science for general audiences—not doctors. Use when the user wants to: (1) Explain clinical trials or research in plain English, (2) Write science content an 8th grader can understand WITHOUT dumbing it down, (3) Create thought leadership for the intelligent public rather than medical peers, (4) Transform complex cardiology findings into stories and narratives, (5) Write pieces where readers DON'T need another LLM to understand the explanation. Maintains full scientific rigor with PubMed citations for verification while avoiding academic language, trial acronyms, and intimidating statistics.
cardiology-youtube-scriptwriter
End-to-end YouTube content creation for cardiology channels. Use when user wants to create YouTube videos about cardiology, heart health, or cardiovascular topics. Triggers on greetings with content intent, requests for video ideas or scripts, help with cardiology YouTube channels, heart health video content requests, or any cardiology content creation conversation. Handles complete workflow from ideation through social listening, topic selection, and full script delivery.
deep-researcher
Performs comprehensive, multi-layered research on any topic with structured analysis and synthesis of information from multiple sources. Uses file-based research tracking, parallel investigation threads, and context-efficient patterns for deep investigations. ALL MEDICAL CITATIONS FROM PUBMED MCP ONLY.
medical-newsletter-writer
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parallel-literature-search
Parallel search across PubMed, Perplexity, and your knowledge base. Searches all sources simultaneously and synthesizes findings with citations. Faster evidence gathering for clinical questions.
perplexity-search
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model's knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
quick-topic-researcher
Rapid topic mastery for video/content prep. Takes a topic → generates 5 research questions → parallel PubMed + web search → outputs McKinsey-style brief in 5 minutes. Use BEFORE recording videos or writing content.
academic-chapter-writer
Comprehensive academic textbook chapter writing system for medical/scientific content. Use when the user wants to: (1) Write a full textbook chapter (5,000-15,000 words) on any medical/scientific topic, (2) Generate a detailed table of contents with section word counts, (3) Research topics via PubMed MCP and compile 20-30 references, (4) Write section-by-section with proper citations in Vancouver format, (5) Create publishable academic content with Eric Topol-inspired voice and authentic human prose, (6) Get approval at TOC stage before writing begins, (7) Export well-structured chapters for textbook publication.
article-extractor
Extract clean article content from URLs (blog posts, articles, tutorials) and save as readable text. Use when user wants to download, extract, or save an article/blog post from a URL without ads, navigation, or clutter.
authentic-voice
Transform AI-sounding writing into natural, human prose. Use when creating or editing any written content—articles, essays, reports, emails, social posts, scripts, or marketing copy—to avoid patterns that signal AI authorship. Triggers on requests to "make it sound human," "less AI," "more natural," improve voice/tone, or any writing task where authentic style matters.
browser-automation
Browser automation for ChatGPT Plus and Gemini Advanced web interfaces. Uses Playwright MCP to interact with your paid subscriptions without API costs. Supports both models for writing comparison.
cardiology-content-repurposer
Transform long-form cardiology content (YouTube transcripts, newsletters, PDFs, knowledge bases) into high-quality thought leadership content across multiple formats. Use when the user wants to repurpose medical/cardiology content into: (1) Short newspaper articles (Inshorts style), (2) Atomic essays, (3) Tweets, (4) Twitter threads, or (5) Medium-style blogs. Maintains authentic interventional cardiologist voice with clinical authority, uses 4A framework, targets specific patient archetypes, and leverages PubMed for evidence-based citations when needed.
cardiology-editorial
Comprehensive cardiology editorial writing system for thought leadership newsletters. Use when the user wants to: (1) Identify and score recent landmark trials from top cardiology journals (NEJM, JAMA, Lancet, JACC, EHJ, etc.), (2) Write evidence-based editorials in Eric Topol's style from Ground Truth, (3) Create 500-word commentaries on clinical trials with PubMed citations, (4) Analyze trial importance using hybrid rules + LLM scoring, (5) Write editorials from full papers OR abstract-only scenarios, (6) Build thought leadership content for cardiologists, or (7) Synthesize recent cardiology advances for peers and referring physicians.
cardiology-newsletter-writer
Create evidence-based cardiology newsletters for thought leadership in Eric Topol's authoritative Ground Truths style. Use when the user wants to analyze trending medical topics with engagement predictions, conduct data-driven topic selection, research medical literature using PubMed, or write comprehensive well-referenced newsletters that build professional authority as an interventional cardiologist. Handles complete workflow from trend analysis to final draft with smooth analytical flow between topics.
cardiology-science-for-people
Write rigorous, accurate cardiology science for general audiences—not doctors. Use when the user wants to: (1) Explain clinical trials or research in plain English, (2) Write science content an 8th grader can understand WITHOUT dumbing it down, (3) Create thought leadership for the intelligent public rather than medical peers, (4) Transform complex cardiology findings into stories and narratives, (5) Write pieces where readers DON'T need another LLM to understand the explanation. Maintains full scientific rigor with PubMed citations for verification while avoiding academic language, trial acronyms, and intimidating statistics.
alphafold-database
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
anndata
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
cirq
Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
dask
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.
pptx
Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.
xlsx
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
fda-database
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
gget
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
hypogenic
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
peer-review
Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.
pylabrobot
Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR, Opentrons OT-2, Tecan EVO), integrating lab equipment, managing deck layouts and resources (plates, tips, containers), reading plates, or creating reproducible laboratory protocols. Applicable for both simulated protocols and physical hardware control.
pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
qiskit
Comprehensive quantum computing toolkit for building, optimizing, and executing quantum circuits. Use when working with quantum algorithms, simulations, or quantum hardware including (1) Building quantum circuits with gates and measurements, (2) Running quantum algorithms (VQE, QAOA, Grover), (3) Transpiling/optimizing circuits for hardware, (4) Executing on IBM Quantum or other providers, (5) Quantum chemistry and materials science, (6) Quantum machine learning, (7) Visualizing circuits and results, or (8) Any quantum computing development task.
research-grants
Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts, significance statements, innovation narratives, and compliance with submission requirements.
research-lookup
Look up current research information using Perplexity's Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, recent studies, technical documentation, and general research information with citations.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
statsmodels
Statistical modeling toolkit. OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference and econometric analysis.
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