aipoch/medical-research-skills.

3d-molecule-ray-tracer

Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.

abstract-summarizer

Transform lengthy academic papers into concise, structured 250-word abstracts.

abstract-trimmer

Precision editing tool that reduces abstract word count through intelligent compression techniques, maintaining scientific rigor while meeting strict journal and conference requirements.

academic-abstract-refiner

Refines long medical academic texts into SCI-style unstructured Chinese and English abstracts; use when you need to condense drafts/reports/summaries into bilingual abstracts and generate Summary_Report.md.

academic-cv-generator

Generate structured academic CVs from free-form Chinese/English text and export to Word (.docx). Use this skill when you are asked to organize, generate, or optimize an academic CV (e.g., publications/projects/awards) into a consistent, formatted document with uniform-colored section headers and optional bilingual output.

academic-highlight-generator

Generates submission-ready Elsevier/SCI Highlights from manuscript text or extracted PDF/DOCX/TXT content. Use when a user needs 3-5 concise, evidence-grounded highlight bullets for a research paper, review, meta-analysis, case report, or bioinformatics manuscript.

academic-norm-review

Detects content similarity, verifies standardized citations and abbreviations, and flags potential academic integrity risks; use it before submission, during academic writing QA, or for compliance reviews.

academic-poster-generator

Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster (beamerposter/tikzposter/baposter) with mandatory figure generation and a final rendered HTML deliverable.

acronym-unpacker

Intelligent medical abbreviation disambiguation tool that resolves ambiguous acronyms using clinical context, specialty-specific knowledge, and document-level semantic analysis.

active-comparator-single-soc-faers-safety-comparison

Generates complete FAERS pharmacovigilance study designs for multi-drug or class-level safety comparison inside one predefined SOC or AE family using active comparators, disproportionality analysis, subgroup characterization, and reviewer-facing evidence control.

adme-property-predictor

Analyze data with `adme-property-predictor` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

adverse-event-narrative

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.

aim-and-hypothesis-designer

Designs primary aims, secondary aims, and testable hypotheses from broad biomedical research ideas. Use this skill when a user needs to convert a loose study idea into a tighter protocol-framing structure with clear aim hierarchy, hypothesis discipline, and separation between hypothesis-driven and exploratory components. Always keep aims answerable, non-overlapping, and aligned to the intended evidence type and study scope.

alphafold-db

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

anatomy-quiz-master

Generate interactive anatomy quizzes for medical education with multiple.

animal-and-cell-validation-planner

Designs cell-based and animal-based validation plans that translate computational, omics, biomarker, genetic, or clinical findings into experimentally testable validation routes. Always use this skill whenever a user wants to move from an in silico, statistical, or clinical association finding toward wet-lab validation using cell systems, organoid-like systems, xenograft or genetically relevant animal models. It should define the exact claim to test, separate mechanism-testing from association-support and translational-support goals, choose the best-fit model family, specify perturbation strategy, readouts, controls, sequencing of experiments, and four workload configurations (Lite / Standard / Advanced / Publication+) with one recommended primary plan. Never fabricate model availability, reagent availability, species relevance, assay feasibility, phenotype penetrance, expected effect sizes, validation success, or literature references.

anki-card-creator

Use anki-card-creator for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries for study-card generation.

api-design-principles

Principles and checklists for designing and reviewing REST and GraphQL APIs; use when defining or evaluating API contracts (endpoints/schemas), naming, error models, pagination, versioning, and REST vs. GraphQL trade-offs.

article-format-adjustment

Adjust academic paper formatting and convert between DOCX/LaTeX/Markdown when you need to meet a journal or school template requirement.

arxiv-database

Search and retrieve scientific preprints from arXiv; use it when you need to find papers by keyword/author/category, fetch metadata (abstract, DOI, PDF URL), or download PDFs for offline reading.

author-response-builder

Turns reviewer comments into structured, professional point-by-point responses linked to manuscript revisions, clarifications, rebuttals, and additional analyses.

authorship-credit-gen

Use when determining author order on research manuscripts, assigning CRediT contributor roles for transparency, documenting individual contributions to collaborative projects, or resolving authorship disputes in multi-institutional research. Generates fair and transparent authorship assignments following ICMJE guidelines and CRediT taxonomy. Helps research teams document contributions, resolve disputes, and ensure equitable credit distribution in academic publications.

automated-soap-note-generator

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.

baseline-extraction-for-clinical-trials

Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full details.

basic-discovery-translational-opportunity-finder

Finds translational opportunities that connect basic-research discoveries to clinically meaningful use cases such as diagnosis, stratification, prognosis, treatment response prediction, monitoring, or therapeutic development. Use this skill when a user wants to turn a mechanism finding, pathway signal, cellular phenotype, experimental observation, or omics discovery into a stronger translational research direction. Always separate mechanistic relevance from translational usability, and never present a basic finding as clinically actionable unless the evidence supports that level.

basic-research-design

A biomedical research topic designer that generates progressive experimental subtitles and detailed research outlines based on a given subject. Use when the user wants to design a research proposal, outline experiments for a topic, or structure a biomedical study.

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bib-formatter

Convert reference lists and in-text citations between RIS, BibTeX, plain text, and CSL-JSON, triggered when you need to unify bibliography/citation styles before journal submission or compare before/after formatting differences.

bibliography

Classifies and organizes literature by theme, method, and conclusion; use when you need to batch-read a folder of PDF/MD/DOCX/TXT files and output a structured CSV for literature reviews and annotation management.

bidirectional-multi-phenotype-mr

Generates complete bidirectional multi-phenotype Mendelian randomization research designs from a user-provided exposure family and outcome family. Always use this skill whenever a user wants to design, plan, or build a genome-wide causal-inference study based on publicly available GWAS summary statistics, especially when the article logic includes multiple exposures, multiple outcomes or subtypes, bidirectional MR, IV filtering, IVW as the main estimator, weighted median / MR-Egger / MR-PRESSO sensitivity analyses, leave-one-out testing, heterogeneity / pleiotropy checks, and multiple-testing control with FDR. Covers five study patterns (single-family bidirectional MR, multi-phenotype screening MR, subtype-resolved MR, phenome-style bidirectional causal map, mechanism-prioritized MR follow-up) 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...

bio-ontology-mapper

Map unstructured biomedical text to standardized ontologies (SNOMED CT.

biodbnet-api

Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.

biogrid-orcs

Accesses BioGRID ORCS CRISPR screen data (organisms, screens, scores). Invoke when user needs to search CRISPR screens, get vocabulary, or retrieve gene scores.

bioinformatics-translational-opportunity-finder

Identifies translationally meaningful paths for bioinformatics findings by mapping omics or computational discoveries to diagnosis, stratification, prognosis, treatment-response, monitoring, or target-nomination use cases, while auditing bridge evidence, assayability, and validation burden. Use this skill when a user wants to know whether a bioinformatics finding can be framed as a stronger translational topic without overclaiming clinical relevance. Always separate statistical signal from translational value, and never imply clinical utility, targetability, or validation depth without explicit evidence support.

biomarker-landscape-scanner

Scans the biomarker landscape of a disease area by biomarker type, clinical/research use case, evidence layer, validation status, and maturity level. Use this skill when a user wants a field-level biomarker evidence map rather than a generic literature summary. Always separate exploratory biomarkers from externally validated or clinically embedded biomarkers, and never imply clinical maturity without explicit evidence support.

biomed-outline-generator

Generates structured biomedical outlines for review articles, discussion sections, and thesis proposals. Use when a user provides biomedical keywords, results/discussion text, or a proposal title plus background and needs a directly usable academic writing scaffold.

biomedical-search-strategy-builder

Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers when the user says "help me search for papers on X", "build a search strategy", "what are the MeSH terms for", or "I need a systematic review search string".

biopython-advanced

Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

biopython-alignment

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

biopython-entrez

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

biopython-phylo

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.

biopython-sequence-io

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.

biopython-structure

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.

biotech-pitch-deck-narrative

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

blind-review-sanitizer

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

blockbuster-therapy-predictor

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

bmi-bsa-calculator

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.

buffer-calculator

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.

bulk-omics-integrative-planner

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.

case-control-study-planner

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

case-control-study-quality-assessment-nos

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.

cellosaurus-api

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.

chart-style-unifier

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.

chea-api

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).

chembl-database

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.

chemical-storage-sorter

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.

chemical-structure-converter

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.

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.

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.

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.

citation-network

Build and visualize a citation network from a source/target CSV to identify key papers, communities, and emerging hotspots; use when you have citation pairs and need fast literature review or trend analysis.

claim-strength-calibrator

Calibrates manuscript claim strength so wording matches the actual evidence level, study design, and validation status.

clinic-research-design

Generates a structured prompt framework for clinical study protocols. Supports Diagnostic, Efficacy, Etiology, and Prognosis studies. Calculates sample size and provides logic guides for LLMs.

clinic-sample-size

Unified tool for calculating sample sizes for Diagnostic, Efficacy, Etiology, and Prognosis clinical studies. Supports various statistical methods (Sensitivity/Specificity, Log-rank, Chi-square, EPV, etc.).

clinical-cohort-protocol-designer

Designs retrospective or prospective clinical cohort study protocols for biomedical and clinical research. Always use this skill when the user needs a cohort-based study plan rather than a general study idea, evidence summary, or mechanistic experiment design. Focus on cohort appropriateness, enrollment logic, baseline time-zero definition, follow-up structure, endpoint definition, variable collection, confounding control, and a coherent primary statistical analysis line. Do not invent data availability, follow-up completeness, outcome ascertainment quality, sample size adequacy, or causal interpretability.

clinical-data-cleaner

Use when cleaning clinical trial data, preparing data for FDA/EMA submission, standardizing SDTM datasets, handling missing values in clinical studies, detecting outliers in lab results, or converting raw CRF data to CDISC format. Cleans and standardizes clinical trial data for regulatory compliance with audit trails.

clinical-question-clarifier

Clarifies a vague clinical or biomedical research idea into a structured, bounded, searchable, researchable, and testable question. Always use this skill whenever a user has an early-stage clinical or research thought, an over-broad topic, an ill-defined evidence question, or an unclear problem statement that must be translated into a question framing suitable for literature retrieval, evidence synthesis, gap analysis, study design, or downstream protocol planning. Never jump straight to answering the substantive medical question unless the user explicitly asks for that. Focus first on question framing, boundary setting, and downstream-ready formulation.

clinical-study-info-extractor

Batch extracts and verifies structured information (PMID, title, abstract, methodology, results, etc.) from clinical research literature using PMIDs. Use when the user wants to extract details from specific PMIDs.

clinicaltrials-db

Query the ClinicalTrials.gov API v2 to search for clinical trials, retrieve detailed study protocols, and analyze recruitment status; use when you need to find trials by condition/drug, export results, or verify study details by NCT ID.

clinicaltrials-gov-parser

Monitor and summarize competitor clinical trial status changes from ClinicalTrials.gov.

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.

co2-tank-monitor

IoT monitoring simulation to predict CO2 tank depletion and prevent weekend gas outages in cell culture facilities. Monitors cylinder pressure, calculates consumption rates, provides early warnings, and supports automated scheduling via cron.

code-refactor-for-reproducibility

Use when refactoring research code for publication, adding documentation to existing analysis scripts, creating reproducible computational workflows, or preparing code for sharing with collaborators. Transforms research code into publication-ready, reproducible workflows. Adds documentation, implements error handling, creates environment specifications, and ensures computational reproducibility for scientific publications.

cohort-study-quality-assessment-nos

Evaluates the quality of cohort studies using the Newcastle-Ottawa Scale (NOS). Use when the user provides a cohort study article or text and needs a quality assessment report.

cold-chain-risk-calculator

Calculate temperature excursion risks for cold chain transport. Assesses route risk, packaging suitability, and monitoring requirements for biological samples and pharmaceuticals requiring controlled-temperature shipping.

comorbidity-common-immune-biomarker

Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Use when a study links two clinically related diseases through shared DEGs, enrichment, PPI hub genes, machine-learning feature selection, public diagnostic validation, gene-regulatory networks, immune infiltration, and optional downstream follow-up. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, machine-learning biomarker selection, immune/regulatory interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

comparative-network-toxicology-shared-mechanism-reference-grounded

Generates complete comparative network-toxicology research designs from a user-provided exposure pair, shared toxic phenotype, and validation direction. Use when a study centers on two related exposures under one outcome and needs target collection, shared-vs-specific target decomposition, enrichment, PPI hub prioritization, docking, optional transcriptomic cross-checks, and conservative mechanistic synthesis. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

comparison-table-gen

Auto-generates comparison tables for concepts, drugs, or study results.

competitor-trial-monitor

Monitor competitor clinical trial progress and alert on market risks.

concept-explainer

Uses analogies to explain complex medical concepts in accessible terms.

conference-abstract-adaptor

Adapt abstracts to meet specific conference word limits and formats.

conference-abstract-writer

Condenses a full study into conference-submission abstract format. Use when adapting a manuscript abstract or study summary to meet a specific conference's word limit, structured format (Background/Methods/Results/Conclusion), character limits, or required section headings. Also triggers on "adapt my abstract for [conference]", "shorten my abstract to 250 words", "reformat for ASCO/ASGCT/SfN/AACR", "I need a conference abstract", or "cut my abstract to fit the word limit".

conference-poster-pitch

Use conference poster pitch for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

conference-tweet-generator

Generates academic conference tweets and summaries by filtering abstracts, translating content, and creating engaging titles. Use when you need to process conference abstracts into social media content.

conflict-of-interest-checker

Check for co-authorship and institutional conflicts between authors and suggested reviewers to support peer review integrity. Coauthorship and institutional conflict detection supported.

confounder-and-bias-control-planner

Plans confounder control, variable adjustment logic, and bias mitigation strategies at the protocol stage for clinical, epidemiologic, translational, observational, and biomarker studies. Always use this skill when a user needs to identify major confounders, decide which variables should or should not be adjusted for, compare matching/stratification/weighting approaches, anticipate selection or measurement bias, or pressure-test a study design before execution. Focus on bias sensing, causal structure awareness, variable-role classification, and critical design review rather than generic statistical advice.

consistency-checker-across-manuscript

Checks consistency across title, abstract, methods, results, figures, tables, and supplements to identify internal contradictions and version drift in biomedical manuscripts.

content-proofreading

An academic proofreading skill for Chinese/English manuscripts, triggered when you need automated checks for spelling, grammar, terminology consistency, and formatting before submission.

contradictory-findings-resolver

Explains why studies on the same biomedical topic reach different or opposing conclusions by auditing differences in population, endpoint definition, sample source, assay or platform, study design, statistical model, adjustment strategy, validation chain, and bias control. It separates true contradiction from apparent contradiction caused by framing or methods. Never fabricate references, PMIDs, DOIs, trial identifiers, dataset details, platform details, study features, or conflict explanations that are not supported by the input.

conventional-non-oncology-hub-gene

Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction. Use when a study centers on multi-dataset bulk transcriptome integration, DEG analysis, process-gene intersection, enrichment analysis, GSEA, PPI hub-gene prioritization, TF/miRNA regulatory networks, ROC-based biomarker evaluation, and immune infiltration analysis. Covers five study patterns (process-DEG discovery, enrichment/GSEA interpretation, hub-gene prioritization, regulatory-network and immune interpretation, multi-layer public validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

conventional-oncology-hub-gene

Generates complete conventional oncology bulk-transcriptome biomarker and hub-gene research designs from a user-provided cancer type and study direction. Always use this skill whenever a user wants to design, plan, or build a tumor bioinformatics study centered on differential expression, prognostic filtering or risk modeling, PPI-based hub-gene prioritization, diagnostic/prognostic evaluation, clinical association, immune infiltration context, methylation context, and optional tissue or cell validation. Covers five study patterns (signature-first prognostic workflow, hub-gene-first biomarker workflow, hybrid signature-to-hub workflow, immune-context biomarker workflow, translational 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...

cover-letter-drafter

Drafts journal-ready cover letters for manuscript submission. Use when preparing a submission package, communicating the manuscript's contributions and journal fit to editors, or tailoring the novelty framing for a specific journal's scope. Also triggers on "write a cover letter for my paper", "draft a submission cover letter", "help me write to the editor", or "cover letter for [journal name]".

cover-letter-generator

Generates a journal-ready cover letter from manuscript metadata, highlights, and journal-fit notes. Use when preparing an academic submission package and you need editor-facing language that clearly states novelty, relevance, declarations, and corresponding-author details.

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.

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.

cross-disease-shared-biomarker-network

Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Always use this skill whenever a user wants to design, plan, or build a multi-dataset study linking two related diseases through shared DEGs, enrichment, PPI hub genes, public validation, regulatory-network analysis, immune infiltration, drug-gene interaction screening, and optional qRT-PCR or cell-line validation. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, regulatory-network interpretation, immune/drug follow-up, bioinformatics-plus-validation) 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, and a strictly verified reference literature retrieval layer with real references only.

crossref-database

Access CrossRef metadata for scholarly works; use when you need to resolve a DOI or search CrossRef to retrieve bibliographic details, citation/reference counts, or funder information for research and citation management.

ctd-api

Accesses Comparative Toxicogenomics Database (CTD) for chemical, gene, disease, and pathway interaction data. Invoke when user needs to query CTD, retrieve toxicogenomics data, or investigate chemical-disease relationships.

date-calculator

Calculate medical date windows including gestational age, estimated delivery dates, and follow-up visit scheduling. Produces structured JSON output for clinical research and trial coordination workflows.

dei-statement-drafter

Draft Diversity, Equity, and Inclusion statements for academic applications.

diagnostic-study-quality-assessment-quadas-2

Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool. Use when Claude needs to assess the quality, risk of bias, or applicability of diagnostic accuracy studies (e.g., "Assess this paper using QUADAS-2").

dicom-anonymizer

De-identify DICOM medical images by removing PHI tags for research sharing, with audit logging and study-linkage preservation support.

diffdock-molecular-docking

Diffusion-based molecular docking to predict 3D ligand–protein binding poses (blind docking) with confidence scoring; use when you need pose prediction for drug discovery or virtual screening.

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.

discharge-summary-writer

Generate hospital discharge summaries from admission data, hospital course.

discussion-composer

Composes a Discussion around key findings, mechanisms, clinical relevance, and limitations. Use when writing or improving a Discussion section for any biomedical manuscript — including interpreting results, connecting to prior literature, addressing unexpected findings, framing limitations, and writing the conclusion. Also triggers on "write my discussion", "help me discuss my findings", "how do I compare to prior studies", "write the limitations paragraph", or "draft a discussion for my paper".

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.

disease-mechanism-evidence-map

Systematically maps mechanism evidence for a disease from molecules to pathways, cell types, tissues, biological consequences, and clinical phenotypes. Always use this skill when a user needs a layered mechanism evidence chain rather than a flat summary or immediate gap analysis. Formal literature citations must be real and verifiable.

docx-feedback-tracker

Automatically detect DOCX track-changes history, version rounds, and author feedback to generate a Markdown modification explanation file when you run it on one or more DOCX versions.

dpi-upscaler-checker

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

drug-interaction-checker

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

drug-repurposing-study-planner

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.

drug-target-evidence-landscape

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.

drugbank-database

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.

dual-disease-shared-transcriptome-biomarker

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...

dual-disease-transcriptomic-ml-planner

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.

ebm-calculator

Evidence-Based Medicine diagnostic test calculator. Computes sensitivity, specificity, PPV, NPV, likelihood ratios, NNT, and pre/post-test probability from 2x2 contingency table inputs.

ectd-xml-compiler

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

ehr-semantic-compressor

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.

emerging-topic-scout

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

encode-api

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.

encori-api

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

endpoint-definition-designer

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.

equipment-maintenance-log

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

evidence-level-ranker

Ranks papers by evidence strength and methodological quality so literature can be compared and prioritized for citation without confusing design labels, validation depth, and actual reliability.

experiment-detail-comparator

Compare experimental method details between two Zotero PDF papers, identify protocol differences (ratios, dosages, timing, conditions), search supporting literature to explain why they differ, and generate an HTML report. Use when you need a parameter-level comparison of two methods and evidence-backed reasons for discrepancies.

experimental-data-analysis

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

expert-interview-generator

Generates a full expert interview article including introduction, Q&A body, and summary based on interview questions and expert background. Use when you have interview questions and an expert profile and need a polished article.

expert-interview-topics

Generates professional interview titles and questions based on expert background and topic. Provides a structured workflow for interview preparation.

facs-gating-viz-style

Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

faers-multi-drug-soc-planner

Generates complete FAERS-based multi-drug single-SOC safety comparison research designs from a user-provided drug set, comparator, and adverse event domain. Always use this skill when users want to compare safety signals across multiple drugs using FAERS or OpenFDA data within one System Organ Class (SOC) or bounded AE domain. Trigger for:"FAERS study comparing drugs within one SOC", "publishable FAERS safety comparison paper", "compare neuropsychiatric adverse events across beta-blockers", "Lite/Standard/Advanced FAERS safety plans", "active-comparator restricted disproportionality", "adjusted ROR logistic regression FAERS", "within-class head-to-head drug comparison", "pharmacovigilance signal comparison", "single-SOC PT-level FAERS design", or any phrasing like "I want to compare drug X and drug Y for adverse events in FAERS" or "build a comparative pharmacovigilance paper". Always output 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.

faers-pharmacovigilance-disproportionality

Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patient-group stratification. Always use this skill whenever a user wants to design, plan, or build a spontaneous-report safety signal study using FAERS or a similar pharmacovigilance database, especially when the article logic includes product selection, indication-group stratification, MedDRA-based adverse-event extraction, serious-case filtering, suspect-drug and concomitant-exclusion logic, reporting odds ratio analysis, comparator-drug benchmarking, cross-drug comparison, and cautious signal interpretation without causal overclaiming. Covers five study patterns (single-drug disproportionality workflow, multi-drug class comparison workflow, indication-stratified workflow, comparator-controlled signal screening workflow...

faq-generator

Generates FAQ lists from complex medical policies or protocols. Trigger when user provides medical documents, policies, or protocols and requests FAQ generation, patient education materials, or simplified explanations.

fastqc-report-interpreter

Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.

fda-guideline-search

Search FDA industry guidelines by therapeutic area or topic.

feasibility-aware-study-planner

Designs a realistic, execution-aware biomedical study version under explicit constraints of samples, time, budget, data access, lab capacity, team skill, and validation resources. Always use this skill when the user has a real study idea, a candidate route, or a partially framed project but cannot assume ideal conditions. If critical feasibility inputs are missing, first clarify what resources are currently available, what resources may be obtainable, and what resources are realistically unavailable. Do not invent access, capabilities, collaborations, or validation resources. Focus first on feasibility-constrained study framing, route narrowing, dependency control, and minimum viable study design.

figure-first-paper-reader

Reads a paper figure by figure before re-integrating the full narrative, so the user can identify the core findings quickly and check whether each visual actually supports the authors' main claims. Always separate figure content, figure-linked claim, evidentiary strength, and unsupported interpretation. Never fabricate references, PMIDs, DOIs, figure content, panel labels, result values, or study details that were not actually provided.

figure-legend-gen

Generate standardized figure legends for scientific charts and graphs.

figure-legend-writer

Writes complete, publication-grade figure legends that can stand on their own. Use when writing or revising figure legends for any scientific figure — bar charts, line graphs, scatter plots, box plots, heatmaps, survival curves, flow cytometry plots, western blots, microscopy images, or schematic diagrams. Also triggers on "write a figure legend for", "help me describe this figure", "my figure needs a legend", "write Figure 1 legend", or "what should a figure legend include".

figure-reference-checker

Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

file-management

Organize, back up, compress, split, and merge files/folders using rule-driven plans; use when you need safe previews, conflict handling, and verification before executing file operations.

file-search

Perform fast file name and content searches with ripgrep (rg); use it when you need to locate files by glob/regex, find keywords across directories, or replace common find/grep workflows.

file-security-toolkit

Encrypt/decrypt local files, redact sensitive information in documents, and validate password strength when handling private data or preparing files for sharing.

forest-plot-styler

Analyze data with `forest-plot-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

fulltext-fetcher

Fetch and save the original HTML of scientific literature webpages when given a URL, DOI, or PubMed PMID (triggered when you need archival-grade page HTML for downstream parsing or review).

funding-trend-forecaster

Analyze funding abstracts and project metadata to identify topic shifts and forecast near-term grant priorities.

gene-info

Retrieves comprehensive gene information including PubMed publication counts, NCBI summaries, and Ensembl transcript data. Supports batch processing and file input. Invoke when the user asks for gene details, publication statistics, or needs to analyze a list of genes.

gene-structure-mapper

Use gene structure mapper for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

generic-phenotype-scoring

Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular program. Use when a study centers on gene-set or feature-set definition, intersection with DEGs or candidate features, phenotype scoring, feature selection, diagnostic or stratification assessment, immune or cellular-resolution interpretation, network analysis, and optional orthogonal validation. Covers five study patterns (signature discovery, phenotype scoring, feature selection, immune/cellular interpretation, multi-layer validation) and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.

geo-search-api

Search for gene expression DataSets and Profiles in the NCBI GEO database. Use this skill when the user wants to find microarray, RNA-seq, or other genomic data by keywords, organism, author, or specific fields.

grant-budget-justification

Use grant budget justification for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

grant-funding-scout

NIH funding trend analysis to identify high-priority research areas.

grant-gantt-chart-gen

Use grant gantt chart gen for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.

grant-mock-reviewer

Simulates NIH study section peer review for grant proposals. Triggers.

grant-specific-aims-writer

Writes Specific Aims pages for grant applications. Use when drafting or revising the Specific Aims page (NIH R01/R21/R03), NSF Project Summary, or equivalent for any major funding agency. Also triggers on "write my specific aims", "help me draft specific aims for NIH", "what should a specific aims page include", "NSF project summary", "write my grant aims", or "how do I structure an R01".

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.

graphical-abstract-generator

Converts a biomedical study storyline into a graphical abstract and, when direct image capability is available, generates the graphical abstract directly; otherwise it falls back to prompts, Mermaid flowcharts, or designer-facing briefs.

graphical-abstract-wizard

Generate graphical abstract layout recommendations based on paper abstracts.

heatmap-beautifier

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

hgnc-api

Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.

high-value-paper-screener

Quickly judges whether a biomedical paper is worth deep reading by screening for question fit, design quality, sample adequacy, methodological novelty, and reproducibility value.

hipaa-compliance-auditor

A clinical-grade PII/PHI detection and de-identification tool for healthcare text data.

hippocrates

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html-to-pdf

Convert HTML files or URLs to high-fidelity PDFs using Puppeteer; auto-detects or forces RTL for Hebrew/Arabic when RTL content is present.

iacuc-protocol-drafter

Draft IACUC protocol applications with focus on the 3Rs principles justification.

ib-summarizer

Summarize core safety information from Investigator's Brochures for clinical.

id-photo-tool

Replace an ID photo background color (blue/white/red) and/or add a configurable text watermark when you need compliant ID-photo variants from local JPG/PNG files.

imagegenskill

Generate renderable, scientific-style SVG graphics directly from natural-language requirements (no image models). Use when users ask for an image/picture/scientific diagram/visualization poster or explicitly request SVG output for web-embeddable vector graphics.

inclusion-exclusion-criteria-builder

Builds clear, executable, and auditable inclusion and exclusion criteria for biomedical and clinical research protocols. Always use this skill when a user needs to translate a target population into operational screening rules tied to chart fields, time windows, tests, procedures, prior therapies, exclusions, and reviewable edge cases. Focus on protocol-stage precision, ambiguity reduction, auditability, and screening reproducibility rather than generic study design advice.

inplasy-registration-helper

Assists researchers in generating INPLASY registration content for meta-analyses from a title and optional protocol. Use when the user wants to draft a INPLASY registration form.

introduction-logic-builder

Builds background-gap-objective logic for biomedical manuscript introductions with clear study positioning and disciplined narrative structure.

introduction-section-writer

Writes the full Introduction section of a biomedical manuscript based on an approved or sufficiently clear study logic, while preserving evidence boundaries and introduction discipline.

irb-application-assistant

Assists researchers with Institutional Review Board (IRB) application tasks, including drafting informed consent documents, reviewing research protocols for compliance, generating application forms, and preparing submission checklists. Use when the user mentions IRB, Institutional Review Board, research ethics, human subjects research, protocol review, informed consent, or needs help preparing or reviewing an IRB application or submission.

jaspar-api

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.

journal-club-presenter

Generate journal club slides with background, critique, and discussion.

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.

journal-impact-factor-trend

Show journal impact factor and quartile trends over 5 years.

journal-latest-issue

Retrieve the latest journal issue's table of contents and abstracts from URL/DOI/PMID/RSS/TOC sources, then generate Chinese key points locally (no external translation APIs) when a new issue needs quick review and archiving.

journal-matchmaker

Analyzes academic paper abstracts to recommend optimal journals for submission, considering impact factors, scope alignment, and domain expertise.

journal-recommender

Recommend academic journals based on manuscript topic, abstract, and impact factor expectations. Use when the user wants to find suitable journals for their research manuscript, especially when they provide a topic, abstract, and target Impact Factor.

journal-skills

Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal recommendation/matching, submission strategy, PubMed search, or similar-literature statistics.

kegg-api

Access the KEGG database API to retrieve biological data (genes, pathways, compounds, drugs). Invoke when the user asks to search, list, or get details from KEGG.

key-takeaways

Extracts and summarizes key takeaways from documents, meeting notes, articles, and other text content. Use when the user asks for summaries, bullet points, main points, highlights, or a TL;DR of any document or body of text. Produces structured outputs such as numbered lists, executive summaries, and action items. Supports configurable output formats including JSON export for downstream use.

keyword-velocity-tracker

Calculate literature growth velocity and acceleration to assess research.

knowledge-base-search

Search and locate relevant content within a local knowledge base (files, indices, or PageIndex). Use when you need verifiable citations (file + page/paragraph) to support answers from local sources.

kv-design

Generate professional Key Visual (KV) design proposals and images; use when you have a slogan/copy and a marketing scenario but need a clear visual direction and a ready-to-generate image prompt.

lab-budget-forecaster

Use lab budget forecaster for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.

lab-inventory-predictor

Predict depletion time of critical lab reagents based on historical usage frequency, and automatically generate purchase alerts when stock falls below safety thresholds.

lab-prep-calculations

Perform pre-experiment calculations and generate step-by-step preparation protocols for dilutions, solution preparation, dissolution, and % concentrations when planning formulations and lab prep workflows.

lab-result-interpretation

A medical assistant tool that transforms complex biochemical laboratory test results into clear, patient-friendly explanations with safety disclaimers and severity flags.

latex-manuscript-format-converter

Converts existing manuscript content into LaTeX format aligned with a target journal, conference, or template while preserving manuscript meaning and structural integrity.

lay-press-release-writer

Transform academic papers into university press releases for general.

lay-summary-for-cross-disciplinary-teams

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lay-summary-gen

Converts complex medical abstracts into plain language summaries for.

learning-tutoring

Learning tutoring planning and content production skill for creating study plans, generating exercises, writing answer explanations, and providing review/adjustment guidance; triggered by requests like “study plan”, “exercise set/question bank”, “answer analysis”, “error analysis”, “exam prep plan”, or “spaced/periodic review schedule”.

limitation-and-risk-writer

Acknowledges limitations in sample, design, measurement, and validation in a professional way that improves credibility without undermining the whole paper. Use when writing the limitations paragraph of a Discussion section, preparing a grant risk assessment, responding to reviewers about study weaknesses, or framing scope boundaries for a paper. Also triggers on "write my limitations", "how should I address the limitation of", "reviewer said my sample is too small", or "help me word this limitation".

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.

lipinski-rule-filter

Filter compound libraries based on Lipinski's Rule of Five for drug-likeness.

litbase

Academic paper reading and research development system for biomedical researchers. Finds papers via Semantic Scholar, reads with structured notes, tracks discussion insights, and synthesizes literature into a Research Foundation Document (RFD) for downstream protocol design skills. 8 commands: /setup /feed /read /discuss /recap /update /sync /propose

literature-close-read

Produce a structured close-reading report from a paper's full PDF-to-Markdown text (with `## Page XX` pagination and image references) when you need to systematically extract background, research questions, methods, results, limitations, and reproducible experimental details.