medical-research-skills

Check if images meet 300 DPI printing standards, and intelligently restore blurry low-resolution images using AI super-resolution technology.

Programmatic access to DrugBank drug and target data; use when you need to download, parse, and analyze DrugBank XML for properties, interactions, pathways, and pharmacology.

Check for interactions between multiple medications, including severity classification and mechanism explanations.

Design evidence-discovery and validation workflows for drug repurposing studies by integrating disease mechanisms, drug-target logic, expression reversal, real-world evidence, and validation routes into a closed-loop study blueprint.

Organizes the evidence and competitive landscape around a drug, target, or pathway by separating disease relevance, tractability, preclinical evidence, clinical evidence, modality fit, and crowding. Always map what is biologically supported, what is druggable, what has actually advanced, and what remains strategically open. Never confuse target relevance with druggability, preclinical activity with clinical promise, or narrative excitement with validated development maturity. Never fabricate references, trial status, approval status, company activity, or asset metadata.

Generates complete dual-disease shared-transcriptome biomarker and hub-gene research designs from a user-provided disease pair and shared-biology direction. Always use this skill whenever a user wants to design, plan, or build a non-oncology two-disease transcriptome study centered on per-disease differential expression, shared-signal intersection or concordance, PPI-based hub-gene prioritization, diagnostic evaluation across both diseases, immune infiltration context, pathway interpretation, and optional orthogonal validation. Covers five study patterns (shared-DEG-first workflow, hub-gene-first shared-biomarker workflow, hybrid shared-biomarker compression workflow, immune-context shared-biomarker workflow, orthogonal validation workflow) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path...

Generates complete dual-disease transcriptomic + machine learning research designs from a user-provided disease pair. Use when users want to identify shared DEGs, common hub genes, cross-disease biomarkers, or shared molecular mechanisms between two diseases using public GEO data. Triggers:"shared biomarker study for two diseases", "dual-disease transcriptomic ML paper", "identify common DEGs between disease A and B", "cross-disease hub gene discovery", "shared DEG + PPI + ROC design", "immune infiltration shared biomarker", or "I want to study disease X and Y together". Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.

Evidence-Based Medicine diagnostic test calculator. Computes sensitivity, specificity, PPV, NPV, likelihood ratios, NNT, and pre/post-test probability.

Automatically convert uploaded drug application documents (Word/PDF) into XML skeleton structure compliant with eCTD 4.0/3.2.2 specifications.

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work. 2. Validate that the request matches the documented scope and stop early if the task would require unsupported as.

Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path and cross-validation plots. Trigger keywords: elastic net, glmnet, feature selection, binary classification, lambda.min, lambda.1se. NOT for: survival/Cox modeling, multiclass outcomes, single-cell data, or non-expression tables.

A real-time monitoring system for identifying "incubation period" research hotspots in biological and medical sciences before they are defined by mainstream journals.

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.

Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Use this skill when the user needs to query ENCODE data, search by keywords, or retrieve specific objects by accession ID.

Access ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data. Invoke when user asks to search ENCORI or retrieve regulatory interactions.

Designs primary, secondary, and exploratory endpoints for biomedical and clinical research protocols. Always use this skill when a user needs to translate study aims into operational endpoint definitions with event rules, assessment timing, composite logic, interpretability, and protocol-stage auditability. Focus on endpoint precision, feasibility, clinical meaning, ambiguity reduction, and implementation readiness rather than generic study design advice.

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

Performs epidemiological analyses including disease modeling (SIR/SEIR), outbreak investigation, risk factor identification, incidence/prevalence estimation, and causal inference from observational data; trigger when users discuss disease spread, public health data, or populat...

Track lab equipment calibration dates and send maintenance reminders for pipettes, balances, centrifuges, and other instruments. Validates date formats and supports update/delete operations.

Toolkit for protein language models (ESM3 for multimodal generative protein design; ESM C for efficient embeddings). Use when you need sequence/structure/function generation or prediction, inverse folding, protein embeddings, or scalable inference via local weights or the Forge API.

Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

Ranks papers by evidence family, methodological quality tier, validation depth, and claim discipline; assigns anchor, context-setting, mechanistic support, or caution citation roles; prevents prestige-based or design-label-based ranking errors.

Statistical analysis and reporting for experimental datasets; use when you need to interpret experimental results, test significance (t-tests/ANOVA), or generate reproducible reports.

Design scientific experiments including sample size calculation, randomization, control groups, blinding, and study protocols. Covers RCTs, quasi-experiments, factorial designs, A/B tests, survey design, and observational studies. Use when user asks to design an experiment, ca...