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.