medical-research-skills

lab-inventory-predictor

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

unstructured-medical-text-miner

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

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.

digital-twin-discharge-drafter

Automatically generates standard discharge summaries mimicking human doctor logic, including admission status, treatment course, and discharge orders for physician audit.

grant-budget-justification

Generate narrative budget justifications for NIH/NSF applications

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.

meta-analysis-forest-plotter

Generate forest plots for meta-analysis with R/Python code

neoantigen-predictor

Predict neoantigens that may be recognized by the immune system based on patient HLA typing and tumor mutation data. Trigger conditions: - User provides HLA typing results and mutation data, requesting neoantigen prediction - User inquires about tumor immunotherapy-related neoantigen prediction - Need to provide T-cell epitope prediction and immunogenicity assessment - Input: HLA alleles (HLA-A*02:01, etc.), tumor mutation data (VCF or peptide sequences) - Output: Predicted neoantigen list, HLA binding affinity, immunogenicity scores

spatial-transcriptomics-mapper

Map spatial transcriptomics data from 10x Genomics Visium/Xenium onto tissue images

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.

pptx-posters

Generate PowerPoint presentations and academic posters from paper content

pseudotime-trajectory-viz

Visualize single-cell developmental trajectories (pseudotime) to show how cells differentiate from stem cells to mature cells. Includes trajectory inference, pseudotime calculation, and publication-ready visualizations.

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.

conference-abstract-adaptor

Adapt abstracts to meet specific conference word limits and formats

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.

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.

phylogenetic-tree-styler

Beautify phylogenetic trees with taxonomy color blocks, bootstrap values, and timeline annotations. Supports Newick format with customizable styling options.

cross-disciplinary-bridge-finder

Discover potential connections between seemingly unrelated disciplines and predict cross-disciplinary innovation opportunities

graphical-abstract-wizard

Generate graphical abstract layout recommendations based on paper abstracts

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.

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.

data-management-plan-creator

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

citation-chasing-mapping

Trace citation networks to discover related research, identify foundational papers, and map field evolution. Analyzes citation relationships to find ancestors (cited works) and descendants (citing works) for comprehensive literature discovery.

volcano-plot-labeler

Automatically label top significant genes in volcano plots with repulsion algorithm

multi-panel-figure-assembler

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

sequence-alignment

Trigger when user needs to align DNA/protein sequences, compare biological sequences, search for similar sequences in databases, or perform BLAST-based similarity analysis. Use for bioinformatics sequence comparison tasks.

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.

interview-mock-partner

Simulates behavioral interview questions for medical professionals.

graph-interpretation

Describes statistical graphs in academic language for manuscripts.

metagenomic-krona-chart

Generate interactive Krona charts (sunburst plots) for metagenomic samples to visualize taxonomic abundance hierarchies. Supports Kraken2, Bracken, Centrifuge output formats.

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.

postdoc-fellowship-matcher

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

in-silico-perturbation-oracle

Virtual gene knockout simulation using foundation models to predict transcriptional changes

heatmap-beautifier

Professional heatmap beautification tool with automatic clustering and annotation tracks

adme-property-predictor

Predict ADME (Absorption, Distribution, Metabolism, Excretion) properties for drug candidates using cheminformatics models and molecular descriptors. Evaluates drug-likeness, bioavailability, and pharmacokinetic profile to guide lead optimization and candidate selection in drug discovery.

flow-cytometry-gating-strategist

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

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.

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)

grant-gantt-chart-gen

Create project timeline visualizations for grant proposals

scrna-cell-type-annotator

Auto-annotate cell clusters from single-cell RNA data using marker genes

volcano-plot-script

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results. Triggered when user needs visualization of gene expression data, p-value vs fold-change scatter plots, publication-ready figures for bioinformatics analysis.

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.

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.

fastqc-report-interpreter

Interpret NGS quality control reports in plain language

dpi-upscaler-checker

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

discussion-section-architect

Guided framework for structuring academic Discussion sections

nih-biosketch-builder

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

survival-curve-risk-table

Automatically align and add "Number at risk" table below Kaplan-Meier survival curves, meeting clinical oncology journal standards. Use when generating risk tables for survival curves that meet top-tier journal standards such as NEJM/Lancet/JCO, automatically calculating the number at risk at each time point.

citation-formatter

Automatically formats academic citations to AMA (American Medical Association) 11th edition style. Converts from APA, MLA, Vancouver, BibTeX, and free-text formats to standardized AMA format for medical and scientific publications.

synthetic-bio-circuit-designer

Design gene circuits for synthetic biology applications

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.

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.

medical-cv-resume-builder

Generates US medical industry standard CVs and resumes.

mentorship-meeting-agenda

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

ecrf-designer

Design clinical trial CRFs with proper validation rules

networking-email-drafter

Draft professional follow-up emails to contacts made at conferences

variant-pathogenicity-predictor

Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity

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.

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.

cnv-caller-plotter

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

crispr-screen-analyzer

Process CRISPR screening data to identify essential genes and hit candidates. Performs quality control, statistical analysis (RRA), and hit calling for pooled CRISPR screens including viability screens and drug resistance/sensitivity studies.

microbiome-diversity-reporter

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

rebuttal-letter-strategist

Strategic response drafting for sharp reviewer criticisms

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.

competitor-trial-monitor

Monitor competitor clinical trial progress and alert on market risks

survival-analysis-km

Generates Kaplan-Meier survival curves, calculates survival statistics (log-rank test, median survival time), and estimates hazard ratios for clinical and biological survival data analysis. Triggered when user requests survival analysis, Kaplan-Meier plots, time-to-event analysis, or asks about survival statistics in biomedical contexts.

gene-structure-mapper

Visualize gene exon-intron structure

presentation-hook

Creates engaging opening statements and powerful closings for medical presentations.

dei-statement-drafter

Draft Diversity, Equity, and Inclusion statements for academic applications

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.

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.

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.

eln-template-creator

Generate standardized experiment templates for Electronic Laboratory Notebooks

table-1-generator

Automated baseline characteristics table generation for clinical papers

poster-layout-planner

Plans layout and content distribution for academic posters.

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.

upset-plot-converter

Convert complex Venn diagrams with more than 4 sets to clearer Upset plots

journal-cover-prompter

Generate AI art prompts for scientific journal cover designs

outlier-detection-handler

Statistical outlier identification and handling recommendations

microscopy-scale-bar-adder

Add scale bars to microscopy images

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.

dashboard-design-for-trials

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

code-refactor-for-reproducibility

Refactor messy R/Python scripts into modular, documented, and reproducible code for top-tier journals

clinical-data-cleaner

Clean and standardize raw clinical trial data for CDISC SDTM compliance. Handles missing values, detects statistical and clinical outliers, validates domain structure, and generates audit trails for regulatory submissions.

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.

q-and-a-prep-partner

Predict challenging questions for presentations and prepare responses

funding-trend-forecaster

Predict funding trend shifts using NLP analysis of grant abstracts from NIH, NSF, and Horizon Europe

linkedin-optimizer

Optimizes LinkedIn profiles for medical professionals.

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.

authorship-credit-gen

Generate standardized author contribution statements following CRediT (Contributor Roles Taxonomy) standards. Creates formal contribution declarations for manuscripts with support for 14 contribution roles, co-first authors, corresponding authors, and multiple output formats for journal submission.

motif-logo-generator

Generate publication-quality sequence logos for DNA or protein motifs to visualize conserved positions and sequence patterns.

conference-poster-pitch

Generate elevator pitch for conference posters

facs-gating-viz-style

Beautify FACS gating plots for publication

study-limitations-drafter

Transform study design flaws into professional limitation statements

alumni-career-tracker

Analyze laboratory alumni career trajectories and outcomes to provide data-driven career guidance for current students and postdocs. Tracks industry vs academia distribution, identifies career pathways, and generates personalized recommendations based on degree level and research interests.

forest-plot-styler

Beautify meta-analysis forest plots with customizable odds ratio points and confidence intervals

cover-letter-drafter

Generates professional cover letters for journal submissions and job applications in medical and academic contexts.

figure-reference-checker

Check figure references in manuscripts

conflict-of-interest-checker

Check for co-authorship conflicts between authors and suggested reviewers