Skills

Professional clinical decision support documents for medical professionals in pharmaceutical and clinical research settings.

"Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis."

"Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis."

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 res

"Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research."

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

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).

"Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis."

"NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization."

"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."

"Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification."

"Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction."

Comprehensive skill for writing competitive research grant proposals focused on four major U.S. funding agencies:

"Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines."

"Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows."

"Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry."

"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."

"Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis."

"Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions."

"Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly."

"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."

"Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control."

Senior FDA consultant and specialist for medical device companies including HIPAA compliance and requirement management. Provides FDA pathway expertise, QSR compliance, cybersecurity guidance, and regulatory submission support. Use for FDA submission planning, QSR compliance assessments, HIPAA evaluations, and FDA regulatory strategy development.

"Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database)."