medical-research-skills

variant-annotation

Query and annotate gene variants from ClinVar and dbSNP databases. Trigger when: - User provides a variant identifier (rsID, HGVS notation, genomic coordinates) and asks about clinical significance - User mentions "ClinVar", "dbSNP", "variant annotation", "pathogenicity", "clinical significance" - User wants to know if a mutation is pathogenic, benign, or of uncertain significance - User provides VCF content or variant data requiring interpretation - Input: variant ID (rs12345), HGVS notation (NM_007294.3:c.5096G>A), or genomic coordinates (chr17:43094692:G>A) - Output: clinical significance, ACMG classification, allele frequency, disease associations

antibody-humanizer

Humanize murine antibody sequences using CDR grafting and framework optimization to reduce immunogenicity while preserving antigen binding. Predicts optimal human germline frameworks and identifies critical back-mutations for therapeutic antibody development.

blind-review-sanitizer

One-click removal of author names, affiliations, acknowledgments, and excessive self-citations from manuscripts to meet double-blind peer review requirements. Preserves document structure while anonymizing sensitive information.

postdoc-fellowship-matcher

Match postdoc applicants to eligible fellowships based on nationality and research area

protein-docking-configurator

Prepare input files for molecular docking software, automatically determine Grid Box center and size. Supports AutoDock Vina, AutoDock4, and other mainstream docking tools.

protein-struct-viz

Generate PyMOL scripts to highlight specific protein residues in PDB structures. Use this skill when the user needs to visualize specific amino acid residues, create publication-quality protein images, or highlight functional sites in protein structures.

survival-curve-risk-table

Generate publication-quality Kaplan-Meier survival curves with aligned "Number at risk" tables meeting NEJM, Lancet, and JCO journal standards.

data-management-plan-creator

Automatically generate NIH 2023-compliant Data Management and Sharing Plan (DMSP) drafts following FAIR principles

scrna-cell-type-annotator

Auto-annotate cell clusters from single-cell RNA data using marker genes, tissue context, and species-specific reference databases.

vector-text-fixer

Fix garbled text in PDF/SVG vector graphics for final editing in AI. Detect, replace and repair garbled text in vector graphic files while maintaining original formatting and layout.

mentorship-meeting-agenda

Generate structured agendas for mentor-student one-on-one meetings

pptx-posters

Generate PowerPoint presentations and academic posters from paper content

resubmission-deadline-tracker

Monitor resubmission deadlines for academic papers and automatically break down tasks based on remaining time. Trigger when user mentions "resubmission deadline", "revision due", "paper deadline", "revise and resubmit deadline", "R&R deadline", or needs to track manuscript revision timelines.

adme-property-predictor

Predict ADME pharmacokinetic properties and drug-likeness of small molecules using validated cheminformatics models. Supports absorption, distribution, metabolism, excretion prediction, QED/MPO scoring, and batch library screening from SMILES input.

flow-cytometry-gating-strategist

Recommend optimal flow cytometry gating strategies for specific cell types and fluorophores

conference-abstract-adaptor

Adapt abstracts to meet specific conference word limits and formats

survival-analysis-km

Kaplan-Meier survival analysis with log-rank tests, Cox regression, and publication-ready survival curves for clinical and biological research.

cross-disciplinary-bridge-finder

Use when identifying collaboration opportunities across fields, finding experts in complementary disciplines, translating methodologies between scientific domains, or building interdisciplinary research teams. Identifies synergies between scientific disciplines, matches researchers with complementary expertise, and facilitates cross-domain collaborations. Supports interdisciplinary grant applications and innovative research team formation.

pseudotime-trajectory-viz

Visualize single-cell developmental trajectories and cellular differentiation processes using pseudotime analysis on AnnData (.h5ad) files.

lab-inventory-predictor

Predict depletion time of critical lab reagents based on experimental usage frequency and automatically generate purchase alerts for laboratory inventory management.

multi-panel-figure-assembler

Automatically assemble 6 sub-figures (A-F) into a high-resolution composite figure with aligned edges, unified fonts, and labels.

volcano-plot-script

Generate publication-ready R or Python volcano plot scripts from DEG analysis results with customizable thresholds, gene labeling, and color schemes.

grant-mock-reviewer

Simulates NIH study section peer review for grant proposals. Triggers when user wants mock review, critique, or evaluation of a grant proposal before submission. Generates structured critique using official NIH scoring rubric (1-9 scale), identifies weaknesses, provides actionable revision recommendations, and produces a comprehensive review summary similar to actual NIH Summary Statement.

discharge-summary-writer

Generate hospital discharge summaries from admission data, hospital course, medications, and follow-up plans. Trigger when user needs to create a discharge summary, compile inpatient medical records, or generate post-hospitalization documentation for patients.

sequence-alignment

Perform sequence alignment via NCBI BLAST API supporting blastn, blastp, blastx, tblastn, and tblastx against major biological databases.

meta-analysis-forest-plotter

Use when creating forest plots for meta-analyses, visualizing effect sizes across studies, or generating publication-ready meta-analysis figures. Produces high-quality forest plots with confidence intervals, heterogeneity metrics, and subgroup analyses.

cnv-caller-plotter

Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, tumor-normal comparison, and BED format export for cancer genomics and rare disease analysis.

grant-gantt-chart-gen

Create project timeline visualizations for grant proposals

upset-plot-converter

Convert complex Venn diagrams with more than 4 sets into clearer UpSet plots for publication-ready set intersection visualization.

crispr-grna-designer

Design CRISPR gRNA sequences for specific gene exons with off-target prediction and efficiency scoring. Trigger when user needs gRNA design, CRISPR guide RNA selection, or genome editing target analysis.

microbiome-diversity-reporter

Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results and generate visualization reports for microbiome analysis.

gene-structure-mapper

Visualize gene structure with exon-intron diagrams, domain annotations, and mutation position markers. Produces SVG, PNG, or PDF figures suitable for publication from a gene symbol input.

ecrf-designer

Design clinical trial CRFs with proper validation rules

blockbuster-therapy-predictor

Predict which early-stage biotechnology platforms (PROTAC, mRNA, gene editing, etc.) have the highest potential to become blockbuster therapies. Analyzes clinical trial progression, patent landscape maturity, and venture capital funding trends to generate investment and R&D prioritization scores. Trigger when: User asks about technology investment potential, platform selection, or therapeutic modality comparison.

fastqc-report-interpreter

Interprets FastQC quality control reports for NGS data. Identifies quality issues, diagnoses root causes, and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq datasets.

neoantigen-predictor

Predict patient-specific neoantigen candidate peptides with high immunogenicity based on HLA typing and tumor mutation profiles, for tumor immunotherapy target screening.

citation-chasing-mapping

Use when identifying seminal papers in a research field, mapping research lineage and intellectual heritage, discovering related work through reference tracking, or finding potential collaborators through co-citation analysis. Maps citation networks to trace research evolution, identify influential papers, and discover hidden connections in scientific literature. Supports systematic reviews, bibliometric analysis, and research planning through comprehensive citation tracking.

nih-biosketch-builder

Generate NIH Biosketch documents compliant with the 2022 OMB-approved format

clinicaltrials-gov-parser

Monitor and summarize competitor clinical trial status changes from ClinicalTrials.gov. Trigger: When user asks to track clinical trials, monitor trial status changes, get updates on specific trials, or analyze competitor trial activities. Use cases: Pharma competitive intelligence, trial monitoring, status tracking, recruitment updates, completion alerts.

in-silico-perturbation-oracle

Virtual gene knockout simulation using foundation models to predict transcriptional changes

dpi-upscaler-checker

Check image DPI and intelligently upscale low-resolution images using super-resolution

abstract-summarizer

Transform lengthy academic papers into concise, structured 250-word abstracts capturing background, methods, results, and conclusions. Optimized for research papers, theses, and technical reports across scientific disciplines.

circos-plot-generator

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. Generates configuration files only — rendering requires Circos installed separately.

graph-interpretation

Use when interpreting scientific graphs and charts, explaining data visualizations for research presentations, writing figure captions for publications, or analyzing trends in clinical research data. Converts complex visual data into clear, accurate explanations for academic papers, clinical reports, and public presentations.

phylogenetic-tree-styler

Beautify phylogenetic trees with taxonomy color blocks, bootstrap values, and timelines. Accepts Newick format and outputs PNG, PDF, or SVG.

citation-formatter

Use when formatting references for journal submission, converting between citation styles (APA, MLA, Vancouver, Chicago), generating bibliographies for manuscripts, or ensuring consistent reference formatting. Automatically formats citations and bibliographies in 1000+ academic styles. Ensures reference accuracy, completeness, and compliance with journal requirements. Supports batch conversion and integration with reference managers.

dei-statement-drafter

Draft Diversity, Equity, and Inclusion statements for academic applications

grant-budget-justification

Generate narrative budget justifications for NIH/NSF applications

adaptive-trial-simulator

Design and simulate adaptive clinical trials with interim analyses, sample size re-estimation, and early stopping rules. Evaluate Type I error control, power, and expected sample size via Monte Carlo simulation before trial initiation.

medical-cv-resume-builder

Generates US medical industry standard CVs and resumes.

interview-mock-partner

Simulates behavioral interview questions for medical professionals.

go-kegg-enrichment

Performs GO (Gene Ontology) and KEGG pathway enrichment analysis on gene lists. Trigger when: - User provides a list of genes (symbols or IDs) and asks for enrichment analysis - User mentions "GO enrichment", "KEGG enrichment", "pathway analysis" - User wants to understand biological functions of gene sets - User provides differentially expressed genes (DEGs) and asks for interpretation - Input: gene list (file or inline), organism (human/mouse/rat), background gene set (optional) - Output: enriched terms, statistics, visualizations (barplot, dotplot, enrichment map)

microscopy-scale-bar-adder

Add scale bars to microscopy images

competitor-trial-monitor

Monitor competitor clinical trial progress and alert on market risks

response-tone-polisher

Polishes response letters by transforming defensive or harsh language into professional, courteous academic prose. Converts phrases like "I will not correct this" into "We respectfully believe the original data sufficiently supports..." to avoid reviewer conflict.

volcano-plot-labeler

Automatically label top significant genes in volcano plots using a force-directed repulsion algorithm to prevent label overlap.

rebuttal-letter-strategist

Strategic response drafting for sharp reviewer criticisms

eln-template-creator

Generate standardized experiment templates for Electronic Laboratory Notebooks

heatmap-beautifier

Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

dicom-anonymizer

Batch anonymize DICOM medical images by removing patient sensitive information (name, ID, birth date) while preserving image data for research use. Trigger when users need to de-identify medical imaging data, prepare DICOM files for research sharing, or remove PHI from radiology/scanned images.

figure-legend-gen

Generate standardized figure legends for scientific charts and graphs. Trigger when user uploads/requesting legend for research figures, academic papers, or data charts. Supports bar charts, line graphs, scatter plots, box plots, heatmaps, and microscopy images. This tool generates text legends only, not visualizations.

presentation-hook

Creates engaging opening statements and powerful closings for medical presentations.

unstructured-medical-text-miner

Mine unstructured clinical text from MIMIC-IV to extract diagnostic logic and treatment details

automated-soap-note-generator

Transform unstructured clinical input (dictation, transcripts, or rough notes) into standardized SOAP (Subjective, Objective, Assessment, Plan) medical documentation. Use ONLY for initial documentation draft generation; ALL output requires physician review before entering patient records. Not for complex cases requiring nuanced clinical reasoning.

motif-logo-generator

Generate publication-quality sequence logos for DNA or protein motifs from FASTA files or raw sequence lists.

variant-pathogenicity-predictor

Integrate REVEL, CADD, PolyPhen-2, SIFT, and MutationTaster scores to predict variant pathogenicity with ACMG guideline interpretation.

metagenomic-krona-chart

Generate interactive Krona charts (sunburst plots) for metagenomic samples from Kraken2, Bracken, or custom TSV taxonomy abundance data.

spatial-transcriptomics-mapper

Map spatial transcriptomics data from 10x Genomics Visium or Xenium onto tissue section images, visualizing gene expression and spatial clustering distributions.

single-cell-rnaseq-pipeline

Generate single-cell RNA-seq analysis code templates for Seurat and Scanpy, supporting QC, clustering, visualization, and downstream analysis. Trigger when users need scRNA-seq analysis pipelines, preprocessing workflows, or batch correction code.

journal-cover-prompter

Use when creating journal cover images, generating scientific artwork prompts, or designing graphical abstracts. Creates detailed prompts for AI image generators to produce publication-quality scientific visuals.

digital-twin-discharge-drafter

Use when drafting patient discharge summaries, creating personalized discharge instructions, simulating post-discharge outcomes, reducing hospital readmissions, or optimizing care transitions. Generates AI-enhanced discharge documentation with digital twin predictions for improved patient safety.

discussion-section-architect

Structures and writes discussion sections for academic papers and research reports. Use when writing a discussion section, interpreting research results, connecting findings to existing literature, addressing study limitations, synthesizing conclusions, or drafting any part of an academic discussion. Helps researchers organize arguments, contextualize data, and produce clear, publication-ready discussion prose.

graphical-abstract-wizard

Generate graphical abstract layout recommendations based on paper abstracts

code-refactor-for-reproducibility

Transforms research code into publication-ready, reproducible workflows. Adds documentation, implements error handling, creates environment specifications, and ensures computational reproducibility for scientific publications.

adverse-event-narrative

Generate CIOMS-compliant adverse event narratives for Individual Case Safety Reports (ICSR). Creates structured pharmacovigilance documents following CIOMS I and ICH E2B standards from case data for regulatory submission to health authorities.

drug-interaction-checker

Check for drug-drug interactions between multiple medications. Trigger when user asks about medication compatibility, "can I take X with Y", drug interactions, contraindications, or safety of combining pharmaceuticals.

poster-layout-planner

Plans layout and content distribution for academic posters.

journal-matchmaker

Recommend suitable high-impact factor or domain-specific journals for manuscript submission based on abstract content. Trigger when user provides paper abstract and asks for journal recommendations, impact factor matching, or scope alignment suggestions.

synthetic-bio-circuit-designer

Design gene circuits for synthetic biology applications

bio-ontology-mapper

Map unstructured biomedical text to standardized ontologies (SNOMED CT, MeSH, ICD-10) for terminology normalization and semantic interoperability. Extracts medical entities and maps to standardized codes with confidence scoring.

networking-email-drafter

Draft professional follow-up emails to contacts made at conferences

peer-review-response-drafter

Assist in drafting professional peer review response letters. Trigger when user mentions "reviewer comments", "response letter", "peer review", "revise and resubmit", "R&R", "reviewer feedback", or needs help responding to academic journal reviewers.

3d-molecule-ray-tracer

Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX to create publication-quality molecular visualizations. Supports ray-tracing, depth of field, ambient occlusion, and cinematic lighting for journal covers and high-impact figures. Use for creating visually compelling protein structure images; not for routine structural analysis or measurements.

table-1-generator

Automated baseline characteristics table generation for clinical papers

crispr-screen-analyzer

Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, log fold change calculation, z-score-based sgRNA scoring, and hit calling for pooled CRISPR screens including viability, drug resistance, and synthetic lethality studies.

clinical-data-cleaner

Clean and standardize clinical trial data to CDISC SDTM standards for FDA/EMA regulatory submissions. Handles missing values, outlier detection, date standardization, and generates audit trails for DM, LB, and VS domains.

outlier-detection-handler

Identify and handle statistical outliers in datasets using z-score, IQR, or Grubbs methods with regulatory-ready documentation.

linkedin-optimizer

Use when optimizing LinkedIn profiles for doctors, physicians, nurses, healthcare professionals, or medical researchers. Crafts compelling headlines, writes professional summaries, integrates healthcare keywords, and builds personal branding for medical careers.

dashboard-design-for-trials

Design dashboard layout sketches for clinical trials showing enrollment progress and adverse event rates