medical-research-skills

Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.

Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.

Use biotech-pitch-deck-narrative for academic writing workflows that need structured investor-facing storytelling, explicit assumptions, and clear output boundaries.

Use blind-review-sanitizer for academic writing workflows that need structured anonymization, explicit assumptions, and clear output boundaries for double-blind submission.

Comprehensive analytics tool for forecasting breakthrough therapeutic technologies by integrating multi-dimensional data sources including clinical development pipelines, intellectual property landscapes, and capital mar.

Calculate Body Mass Index (BMI) and Body Surface Area (BSA) for clinical assessment, obesity screening, and chemotherapy dosing. Supports multiple BSA formulas (DuBois, Mosteller, Haycock), WHO weight classification, pediatric calculations, and metric/imperial input.

Creative exploration and brainstorming; use it when you need to clarify goals/constraints, explore multiple options, and converge on a direction before implementation.

Programmatic access to the BRENDA enzyme database via the SOAP API; use when you need kinetic constants (Km, kcat, Vmax), reaction equations, enzyme properties (pH/temperature optima, stability), or enzyme discovery by EC/substrate/product.

Calculate precise buffer recipes with accurate mass and volume measurements for molecular biology and biochemistry. Supports PBS, RIPA, and TAE with concentration scaling, stock solution preparation, pH adjustment guidance, and step-by-step protocols.

Designs complete integrated research plans for bulk transcriptomics, proteomics, metabolomics, and related omics from a user-provided biomedical direction. Always use this skill whenever a user wants to design, scope, or structure a bulk multi-omics or single-omics-plus-clinical study — including disease-focused, mechanism-focused, biomarker-focused, stratification-oriented, or translational projects. It should define the research question, choose the best-fit study pattern, recommend example datasets as reference candidates only, specify the core analysis modules and method choices, propose a validation ladder, and output four workload configurations (Lite / Standard / Advanced / Publication+). Never fabricate datasets, accession numbers, sample counts, metadata completeness, cohort availability, assay coverage, literature references, PMIDs, DOIs, or validation status. Always include the mandatory Dataset Disclaimer immediately before any workflow section that mentions datasets or public resources.

Design a structured case-control study framework with explicit source population logic, control selection rules, matching decisions, exposure measurement planning, and bias-control checkpoints.

Clinical Research Bias Assessment - Case-Control Study (NOS) v2.3.0. Use when you need to assess the bias of a case-control study using the Newcastle-Ottawa Scale (NOS) criteria, or when evaluating the quality of a medical paper.

Access Cellosaurus database for cell line information and release data. Invoke when user asks to search cell lines, get cell line details by accession, or check database release info.

Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.

Use when building a ceRNA regulatory network from a key gene list by combining bundled miRNA-mRNA and miRNA-lncRNA database files, with flat-file CSV exports and PDF visualization in a single output directory. NOT for: differential expression, single-cell analysis, enrichment analysis, or workflows without a key gene list.

Batch-unify typography (font family, size, italics) for Word table cells and embedded charts; use when you need consistent formatting across theses/reports without changing body text.

Access ChEA3 and Harmonizome ChEA data for transcription factor enrichment analysis and metadata retrieval. Use when the user needs to perform ChEA3 enrichment analysis on a gene set, get metadata about the ChEA dataset, or retrieve information about a specific transcription factor (attribute).

Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure (SMILES), or retrieve drug mechanism information.

Sort laboratory chemicals into safe storage groups by hazard classification (acids, bases, oxidizers, flammables, toxics). Identifies incompatible pairs, generates storage plans with warnings, and supports OSHA/NFPA compliance for lab safety.

Convert between IUPAC names, SMILES strings, molecular formulas, and common names for chemical compounds. Supports SMILES validation, batch processing, structure standardization, and cheminformatics database preparation for drug discovery workflows.

Use when estimating relative immune cell infiltration from a bulk expression matrix with a CIBERSORT-style nu-SVR deconvolution workflow based on an LM22 signature matrix, comparing one case group against one control group, and generating structured tables plus immune-fraction plots. NOT for single-cell RNA-seq, spatial data, clinical diagnosis, or workflows that require the original hosted CIBERSORT web service.

Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots.