aipoch
535 verified skills40,439 total stars
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...
tools348
reporting-guideline-compliance-checker
Checks biomedical manuscripts against reporting guidelines such as CONSORT, STROBE, PRISMA, and TRIPOD to identify missing or weak reporting elements before submission or revision.
testing348
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.
development348
author-response-builder
Turns reviewer comments into structured, professional point-by-point responses linked to manuscript revisions, clarifications, rebuttals, and additional analyses.
development348
paper-to-claim-verifier
Verifies whether a scientific or biomedical claim is actually supported by the cited original papers rather than by citation drift, overstatement, selective citation, or correlation-to-causation inflation. Use this skill whenever a user wants to check whether a repeated statement, slide claim, manuscript sentence, review assertion, or “people often say” scientific conclusion is truly supported by the underlying primary literature. Always separate the claim itself, the cited paper(s), what the paper actually showed, what it did not show, and whether later retellings drifted beyond the original evidence. Never fabricate references, findings, study features, or citation chains.
testing348
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.
testing348
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.
testing348
result-reliability-checker
Assesses whether study results are trustworthy by auditing design integrity, sample structure, statistical handling, bias control, validation chain, and claim discipline. It identifies where results are robust, fragile, overfit, under-validated, or overclaimed. Always separate reported findings from reliability judgment. Never fabricate references, PMIDs, DOIs, trial identifiers, study features, or validation claims.
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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".
development348
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]".
testing348
methods-section-writer
Turns your protocol and analysis workflow into publication-ready Methods text. Use when writing or revising the Methods section of a biomedical manuscript, ensuring it complies with reporting guidelines (CONSORT, STROBE, PRISMA, TRIPOD), matches what is in the Results section, and satisfies journal-specific word limits and declarations. Also triggers on "write my methods", "revise my methods section", "how to report my statistics", "what do I need to include in methods for [study type]", or "make my methods CONSORT-compliant".
testing348
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.
testing348
introduction-logic-builder
Builds background-gap-objective logic for biomedical manuscript introductions with clear study positioning and disciplined narrative structure.
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results-section-structurer
Organizes biomedical figures, analyses, and result blocks into a clear Results section structure with disciplined narrative ordering and evidence-aware presentation.
testing348
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.
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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.
testing348
topic-evidence-mapper
Rapidly maps the evidence landscape around a medical topic by organizing major research streams, target populations, endpoints, methods, evidence density, and thin areas. Use this skill BEFORE medical-research-gap-finder — it provides the structured landscape that makes formal gap analysis more rigorous. Do not use for formal gap identification, study design, or protocol planning directly.
development348
multi-database-literature-collector
Collects candidate biomedical literature across multiple databases, adapts search logic by database, preserves source metadata, and organizes results into a structured, screening-ready candidate pool. Always use this skill when a user wants cross-database literature collection, search strategy construction, candidate paper aggregation, or first-pass evidence organization before deduplication, screening, layered reading, or review planning. Requires real and verifiable literature records only. Every formal literature item must include a real link and DOI when available; never fabricate citations, titles, authors, years, journals, abstracts, PMIDs, or DOIs. If a DOI is unavailable or cannot be verified, state that explicitly rather than inventing one.
testing348
unmet-clinical-need-extractor
Extracts concrete unmet clinical needs from guidelines, reviews, real-world studies, and clinical-practice evidence. Use this skill when a user wants to turn broad medical research value into specific clinical pain points such as weak early detection, poor risk stratification, treatment-response heterogeneity, monitoring gaps, diagnostic delay, undertreatment, overtreatment, or implementation failure. Always ground unmet-need claims in retrieved evidence and distinguish true care gaps from generic statements of importance.
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claim-strength-calibrator
Calibrates manuscript claim strength so wording matches the actual evidence level, study design, and validation status.
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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".
documentation348
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.
testing348
medical-topic-saturation-and-whitespace-checker
Maps whether a biomedical research topic, subtopic, or study angle is truly saturated, superficially crowded, strategically occupied, or still open for differentiated entry. Use this skill when a user wants to know whether a hot medical research direction is already overworked, whether meaningful whitespace remains, whether major groups have already occupied the obvious claims, and whether the timing window is still open. Always distinguish popularity from true saturation, and distinguish cosmetic novelty from meaningful differentiating entry.
testing348
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".
testing348
poster-storyline-builder
Reorganizes a paper into a storyline suitable for scientific posters. Use when planning the section structure, title hierarchy, figure selection, and live-explanation flow for an academic conference poster. Also triggers on "help me design a poster layout", "what sections should my poster have", "how do I arrange my poster", "poster structure for [conference]", or "which figures should I use for my poster".
development348
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.
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results-section-writer
Writes the full Results section of a biomedical manuscript from a sufficiently clear result structure, figure inventory, or analysis summary while preserving evidence boundaries and result hierarchy.
testing348
revision-strategy-planner
Builds prioritized manuscript revision plans for major or minor revisions by separating comments that require experiments, analyses, clarification, restructuring, or wording changes.
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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.
testing348
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".
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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.
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method-gap-detector
Detects methodological gaps across study design, analysis, validation, bias control, reproducibility, and implementation readiness within a biomedical research area. Use this skill when a user wants to identify what current studies are still methodologically missing, which weaknesses are most consequential, and what upgrade path would produce a stronger next-step study. Always separate design gaps, analysis gaps, validation gaps, and reproducibility gaps. Never treat technical complexity as methodological rigor.
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study-design-identifier
Identifies the real underlying study design used in a medical or biomedical paper, distinguishes primary and secondary design components when papers are hybrid, and converts the paper into an evidence-aware design label suitable for literature appraisal, evidence grading, and downstream review workflows. Always identify the actual design from what the study did, not from how the authors describe it. Never fabricate references, metadata, or study features.
data-ai348
slide-deck-for-lab-meeting
Structures research progress into focused and actionable slides for lab meetings or project reviews without inventing missing content.
content-media348
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.
testing348
methods-reverse-engineer
Reverse-engineers the methods section of a biomedical paper into a structured, reproducible workflow. Use this skill when a user wants to understand how a study was actually executed, extract data sources, inclusion/exclusion logic, preprocessing, analytical sequence, software/tools, validation path, and critical parameters, or build a replication checklist from a paper, abstract, DOI, PMID, title, screenshot, or partial methods text. Do not treat this as generic summarization. Focus on reconstructing the operational method pipeline, surfacing missing reproducibility details, and distinguishing explicitly reported steps from inferred or unresolved ones. Never fabricate references, methods details, identifiers, software versions, parameters, datasets, or validation steps.
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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.
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medical-english-precision-editor
Improves medical English precision without changing the underlying facts, evidence boundaries, or intended scientific meaning.
testing348
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.
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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...
development348
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.
development348
table-narrative-writer
Converts biomedical table content into clear manuscript or presentation narrative by prioritizing meaningful patterns, contrasts, and interpretation boundaries rather than restating every number.
documentation348
title-and-abstract-optimizer
Optimizes manuscript titles and abstracts for information density, factual accuracy, and submission fit in biomedical research writing.
development348
evidence-level-ranker
Ranks papers by evidence family, methodological quality tier, validation depth, and claim discipline; assigns anchor, context-setting, mechanistic support, or caution citation roles; prevents prestige-based or design-label-based ranking errors.
testing348
novelty-vs-feasibility-assessor
Assesses whether a medical research topic is worth starting now by separating true novelty from pseudo-novelty, auditing real feasibility under stated resource constraints, and forcing a concrete start / narrow / redesign / stop decision. Always require explicit assumptions and never fabricate references, datasets, resource availability, precedent studies, or publication claims.
testing348
reference-integrity-checker
Checks whether manuscript references are accurately matched to claims, appropriately scoped, and not overextended, misquoted, or second-hand cited.
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lay-summary-for-cross-disciplinary-teams
Rewrites technical research content into a structured lay summary that cross-disciplinary teams can quickly understand and act on. Use when the user wants to explain research to colleagues outside their specialty — clinicians, wet-lab scientists, bioinformaticians, product managers, or leadership. Trigger on: "lay summary", "explain my research to the team", "non-technical summary", "cross-disciplinary summary", "translate my findings", "align our team on the study", or any request to communicate research goals, findings, or next steps to a mixed or non-specialist audience. Part of the AIPOCH Academic Writing skill hub. Sits midstream: after research content is clarified, before downstream deliverables like slide decks or graphical abstracts.
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bianque
Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology, differential diagnosis, medical literature appraisal, and the philosophy of early intervention. Trigger whenever users ask about medicine, clinical science, drugs, disease mechanisms, diagnosis, lab interpretation, treatment comparison, or health sciences. Even without explicit research framing, trigger on any topic touching disease, therapeutics, or clinical decision-making. Part of the AIPOCH Medical Research Skill Hub.
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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".
development348
population-gap-detector
Detects overlooked, underrepresented, weakly resolved, or poorly validated populations and subgroups within a biomedical research area so users can identify more precise and meaningful study populations. Always use this skill when the real question is not just what is under-studied, but which populations, strata, or subgroups are missing, thinly represented, superficially analyzed, pooled without resolution, or insufficiently validated in the current evidence base. Focus on meaningful subgroup gaps rather than generic calls for diversity.
testing348
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
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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.
testing348
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.
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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.
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preprint-surveillance-finder
Tracks the latest preprints and emerging research topics related to your topic across bioRxiv, medRxiv, and arXiv. Use when a user wants to discover what is being published right now before it reaches journals, monitor competitor directions, spot new methodology trends, or get an early-warning scan of a research area. Triggers on phrases like "what's new in X", "latest preprints on Y", "emerging topics in Z", "monitor bioRxiv for", or "what are people working on in this field".
testing348
target-journal-matcher
Matches your study to appropriate journals based on topic, design, and evidence strength. Use when deciding where to submit a manuscript, comparing journal options by impact factor vs scope fit vs method tolerance, or finding a realistic submission target after a rejection. Also triggers on "where should I submit this paper", "which journal is best for my study", "find journals for my manuscript", "is this a good fit for [journal]", or "I need a journal with IF around X".
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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.
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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.
tools348
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".
testing348
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.
testing348
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.
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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.
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medical-research-gap-finder
Identifies real, evidence-audited, topic-specific research gaps in medical research by first retrieving and verifying literature from trusted sources, then mapping the current evidence landscape, rejecting pseudo-gaps, and converting only medium/high-confidence gaps into study-ready research opportunities. Always require real literature retrieval before formal gap claims. Never fabricate references, metadata, or findings.
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medical-research-literature-reader-pro
A medical-research-native literature reading skill for users with clinical, bioinformatics, translational, and basic experimental backgrounds. Use this skill whenever a user wants to read, analyze, critique, or interpret a medical or scientific paper — whether they provide a PDF, abstract, DOI, PMID, or just a title. Triggers include requests like "analyze this paper", "critique this study", "is this a strong paper?", "give me similar studies", "prepare me for journal club", "help me understand this bioinformatics paper", "what are the weaknesses here?", or "turn this into a mind map". Also activate for any downstream deliverables such as journal club kits, comparison tables, PI decision briefs, replication starters, or follow-up experiment designs. Do NOT treat as a generic summarizer — this skill performs structured evidence-type classification, track-specific critical appraisal, interpretation-boundary judgment, and research-grade follow-up generation.
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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.
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mendel
Gregor Mendel — genetics mentor, patient experimenter, and gardener-monk. Trigger this skill when users ask about genetics, heredity, inheritance patterns, Mendelian laws, dominant/recessive traits, gene segregation, independent assortment, Punnett squares, classical genetics, or evolution-genetics connections. Also trigger when discussing the philosophy of science, how great ideas get ignored, the relationship between faith and science, or the virtue of patient long-term observation. Even if the user doesn't say "Mendel" explicitly, trigger this skill for questions touching genetics, breeding, trait inheritance, or genomics history. Part of the AIPOCH Science Mentor Skill Hub.
development348
paper-sprint-review
Scrum-inspired paper review, revision, and R&R workflow. Handles docx/tex/md/PDF in English or Chinese. Auto-detects manuscript stage, estimates sprint count, runs multi-lens review (Contribution/Rigor/Writing/Editor), generates prioritized revision backlog, exports MD/DOCX/PDF/HTML reports. Use when asked to review a paper, revise based on reviewer comments, handle R&R, respond to peer review, plan paper revision sprints, or when user types /ps or /papersprint.
development155
openalex-db
Access the OpenAlex database (240M+ scholarly works) for bibliometric analysis, literature search, and citation tracking; use when you need to query works/authors/institutions/concepts without an API key.
development37
patent-claim-mapper
Use when mapping patent claims to products, analyzing patent infringement, or preparing freedom-to-operate analyses. Compares patent claims against product features for biotech and pharmaceutical IP assessment.
data-ai37
pathway-introduction-expert
Generates comprehensive academic introductions for biological pathways, including signaling processes, markers, and inhibitors. Use when the user asks to introduce a pathway, molecule, or gene.
research37
pdf-extract-experimental-materials
Extract experimental materials and instrument information from PDFs (or PDF-derived text/Markdown) into three CSV tables; use when a paper/report contains sections like Materials and Methods, Key Resources Table, Reagents, Antibodies, Consumables, Software, Equipment, Instruments, or Reagent Preparation.
development37
pubchem-database-skill
Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure searches, and obtaining bioactivity data.
development37
pubmed-search-specialist
Build complex Boolean query strings for precise PubMed/MEDLINE literature retrieval. Trigger when user needs MeSH term mapping, Boolean query construction, advanced PubMed filters, citation searching, systematic review search strategy, or clinical query optimization.
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pytdc
Therapeutics Data Commons (PyTDC) for AI-ready therapeutic ML datasets and benchmarks; use it when you need standardized dataset loading, meaningful splits (e.g., scaffold/cold-start), and consistent evaluation for ADME/Toxicity/DTI/DDI or molecular optimization.
testing37
pubmed-topic-recommend
Generate ~5 actionable research topic recommendations by querying PubMed E-utilities; use when a user provides a research direction/constraints and needs evidence-backed topic ideas quickly.
data-ai37
research-article-weekly
Generates a weekly academic literature report based on keywords using PubMed. Use when the user wants to track recent research progress on a specific topic, automatically retrieving, classifying, and summarizing relevant papers from the last 7 days.
testing37
retraction-watcher
Automatically scan document reference lists and check against Retraction.
testing37
sop-writer
Write GCP-compliant Standard Operating Procedures for labs and clinical sites
tools37
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.
tools37
PPTX Skill
Create, edit, and extract content from PowerPoint (.pptx) files; use when you need to generate slides programmatically, update existing decks, or export slide previews.
content-media37
audio-script-writer
Convert written medical content into podcast or video scripts optimized for audio delivery. Transforms academic papers, reports, and educational materials into engaging spoken-word formats with pronunciation guides, timing markers, and audio-friendly structure.
development37
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.
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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.
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clinical-reports
Write comprehensive clinical reports (case reports, diagnostic reports, clinical trial reports, and patient documentation) when accuracy, regulatory compliance (HIPAA/FDA/ICH-GCP), and template-driven validation are required.
tools37
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.
data-ai37
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.
testing37
datamol
A Pythonic wrapper around RDKit with simplified interfaces and sensible defaults. Preferred for standard drug discovery workflows including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformer generation, and parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
development37
dpi-upscaler-checker
Check if images meet 300 DPI printing standards, and intelligently restore blurry low-resolution images using AI super-resolution technology.
testing37
expert-interview-topics
Generates professional interview titles and questions based on expert background and topic. Provides a structured workflow for interview preparation.
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grammar-checker-ama
Grammar checking tool for AMA style medical writing
tools37
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.
development37
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.
tools37
iso-13485-certification
A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS. Use when you need to perform a documentation gap analysis, draft or update a Quality Manual, create required procedures/work instructions, build Medical Device Files (MDF), interpret ISO 13485 clauses, or identify missing documents for certification (often triggered by ISO 13485, QMS certification, FDA QMSR, EU MDR, or quality system documentation requests).
tools37
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”.
testing37
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.
tools37
medication-reconciliation
Compare patient pre-admission medication lists with inpatient orders to automatically identify omitted or duplicated medications and improve medication safety.
testing37
mindmap-helper
Organize requirements into Markdown/JSON mind map structures; use when you need a hierarchical outline for mind map tools (e.g., XMind, ProcessOn, FreeMind) or for documentation planning.
tools37
note-summarizer
Organize study notes into a structured knowledge-point outline and export to a .docx summary when you need a shareable, hierarchical document from Word/PPT/Text/Markdown inputs.
documentation37
pdf-ppt
Create literature-report PPTX decks from PDF papers. Use when you must extract a paper’s metadata, summarize the study, interpret Results/Figures/Tables, and generate slides with 1:1 figure-to-text alignment and layout rules (triggered by requests like “PDF to PPT”, “literature report slides”, or “turn this paper into a presentation”).
data-ai37
pdf-processor
Perform basic local PDF operations (merge, split, extract pages/text/tables, create) when users request offline PDF processing without external services.
content-media37
pdf-to-ppt-pack
Convert research paper PDFs into literature-report PPTX decks using a fully offline workflow (extract text/figures, map captions, summarize findings, and generate slides). Use when you need to turn a PDF into a presentation deck, especially for scientific articles with figures and tables.
testing37
ppt
Create and export PPTX decks using the local HTML/JS PPT framework in `D:\SKILL\project\ppt`. Use this when you need to generate slides from a topic/outline, edit slide content via `projects/*.js`, preview as HTML, or export a `.pptx` without relying on an existing template.
development37
ppt
Create and export PPTX decks using the local HTML/JS PPT framework in `D:\SKILL\project\ppt`. Use this when you need to generate slides from a topic/outline, edit slide content via `projects/*.js`, preview as HTML, or export a `.pptx` without relying on an existing template.
development37
scientific-schematics
Automates publication-quality scientific diagrams (e.g., flowcharts, architectures, pathways) when you need journal/poster-ready visuals from a natural-language description.
testing37
text-format-organizer
A local text formatting organizer for biomedical/academic writing; use it when you need to clean whitespace/line endings while preserving Markdown structures or when normalizing .docx/.md/.txt before submission or proofreading.
development37
text-to-technical-roadmap
Converts research text into a Mermaid technical roadmap flowchart. Use when the user provides research proposals, experiment designs, or scientific text and asks for a roadmap or flowchart.
testing37
virtual-patient-roleplay
Simulate standardized patient encounters for medical training, supporting OSCE-style history-taking practice, communication skills rehearsal, and educational debriefing.
data-ai37
inclusion-criteria-gen
Generate and optimize clinical trial subject inclusion/exclusion criteria to balance scientific rigor with recruitment feasibility. Trigger when users need to design eligibility criteria for new trials, optimize existing criteria for better enrollment, analyze competitor trial eligibility patterns, or assess recruitment barriers. Use cases: Protocol design, eligibility optimization, recruitment strategy, competitive eligibility analysis, feasibility assessment.
tools37
randomization-gen
Generate block randomization lists for RCTs
tools37
methodology-extractor
Batch extraction of experimental methods from multiple papers for protocol.
research37
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.
testing37
literature-statistics
Generate statistics for publication-year and journal distributions from local references or PDFs; use when you need standardized Year/Journal tables and a summary without any network access.
content-media37
abstract-trimmer
Precision editing tool that reduces abstract word count through intelligent compression techniques, maintaining scientific rigor while meeting strict journal and conference requirements.
tools37
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.
development37
adme-property-predictor
Analyze data with `adme-property-predictor` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
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.
development37
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.
tools37
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.
research37
biopython
A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.
tools37
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.
development37
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.
development37
bioservices
Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.
development37
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.
testing37
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.
tools37
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.
testing37
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.
development37
conference-abstract-adaptor
Adapt abstracts to meet specific conference word limits and formats.
development37
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.
testing37
cobrapy
Constraint-based reconstruction and analysis (COBRA) for metabolic models; use when you need to simulate growth/production, analyze flux ranges, or run knockout and medium studies from SBML/JSON/YAML models.
data-ai37
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.
testing37
grant-mock-reviewer
Simulates NIH study section peer review for grant proposals. Triggers.
research37
dei-statement-drafter
Draft Diversity, Equity, and Inclusion statements for academic applications.
research37
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").
tools37
discharge-summary-writer
Generate hospital discharge summaries from admission data, hospital course.
documentation37
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.
documentation37
scientific-skills/Protocol Design/dual-disease-transcriptomic-ml-planner
--- name: dual-disease-transcriptomic-ml-planner description: 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
testing37
flowio
Parse Flow Cytometry Standard (FCS) files v2.0–3.1 and extract events/metadata for preprocessing workflows (e.g., when you need NumPy arrays, channel info, or CSV/DataFrame export from cytometry files).
data-ai37
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.
testing37
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.
testing37
figure-legend-gen
Generate standardized figure legends for scientific charts and graphs.
testing37
figure-reference-checker
Use figure reference checker for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
forest-plot-styler
Analyze data with `forest-plot-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
geniml
Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run similarity search and downstream ML on chromatin accessibility datasets.
tools37
graphical-abstract-wizard
Generate graphical abstract layout recommendations based on paper abstracts.
research37
heatmap-beautifier
Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.
tools37
gtars
A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML, reference sequence verification, or fragment processing.
tools37
hipaa-compliance-auditor
A clinical-grade PII/PHI detection and de-identification tool for healthcare text data.
tools37
histolab
Lightweight Whole Slide Image (WSI) tiling and preprocessing for digital pathology; use when you need fast tissue detection and tile extraction to prepare datasets or run quick tile-based analysis.
data-ai37
iacuc-protocol-drafter
Draft IACUC protocol applications with focus on the 3Rs principles justification.
testing37
hypogenic
Automated LLM-driven hypothesis generation and testing for tabular datasets; use when you need systematic exploration of empirical patterns (e.g., fraud detection, content analysis) and want to combine literature insights with data-driven hypothesis evaluation.
testing37
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.
tools37
market-access-value
Use market access value for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
lab-budget-forecaster
Use lab budget forecaster for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
lay-press-release-writer
Transform academic papers into university press releases for general.
documentation37
lay-summary-gen
Converts complex medical abstracts into plain language summaries for.
data-ai37
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.
development37
matchms
Process, clean, and compare mass spectrometry (MS/MS) spectra with Matchms; use when you need reproducible spectral filtering and similarity scoring for metabolomics workflows.
testing37
mechanism-flowchart
Generates Mermaid flowchart code and visual diagrams for pathophysiological.
development37
medical-cv-resume-builder
Use medical cv resume builder for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
development37
medical-email-polisher
Transforms rough email drafts into polished, professional medical correspondence.
data-ai37
medical-translation
Use medical translation for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
meta-analysis-methods-generator
Generates the Methods section for a meta-analysis paper, including search strategy, screening, quality assessment, data extraction, and statistical analysis.
testing37
meta-baseline-generator
Generates a meta-analysis baseline characteristics section (text + table) from raw data. Supports Chinese and English. Use when the user provides baseline data and wants a formatted results section.
development37
metabolomics-workbench-database
Access NIH Metabolomics Workbench (4,200+ studies) via REST API. Query metabolites, RefMet nomenclature, MS/NMR data, m/z search, study metadata for metabolomics and biomarker discovery.
development37
meta-feasibility-analyzer
Analyzes the feasibility of a proposed Meta-analysis topic by searching for existing Meta-analyses and Clinical Trials on PubMed/ClinicalTrials.gov. Use when you need to evaluate if a topic is viable for a new Meta-analysis.
tools37
meta-funnel-plot
Generate Meta-analysis funnel plots and perform publication bias testing. Takes CSV file with Meta-analysis data as input, outputs funnel plot PNG, Egger test and Begg test results.
testing37
meta-manuscript-generator
Generates a first draft of a clinical meta-analysis paper. Input the research report (including Methods and Results sections), language, and title to automatically generate a complete paper draft including Abstract, Introduction, Discussion, and other sections, with automatic PubMed retrieval of relevant references. Suitable for assisting in the writing of systematic reviews and meta-analyses.
tools37
meta-protocol-writer
Generates a PROSPERO-compliant Meta-analysis protocol based on Title and PICOS. Use when the user wants to write a protocol for a systematic review or meta-analysis.
documentation37
meta-results-risk-of-bias
Generates the "Risk of Bias" results section for a meta-analysis based on assessment tables and statistics. Use when the user wants to draft the risk of bias analysis text from provided data tables.
data-ai37
neuropixels-analysis
End-to-end Neuropixels extracellular electrophysiology analysis (SpikeGLX/Open Ephys/NWB) including preprocessing, motion correction, Kilosort4 spike sorting, QC metrics, and Allen/IBL-style curation; use when processing Neuropixels recordings or when users mention Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, drift/motion correction, or unit curation.
testing37
microbiome-diversity-reporter
Interpret Alpha and Beta diversity metrics from 16S rRNA sequencing results.
testing37
moa-explainer
Generate 3D animation scripts and lay explanations for drug mechanisms.
data-ai37
motif-logo-generator
Generate publication-quality sequence logos for DNA or protein motifs.
development37
neurokit2
Comprehensive biosignal processing for ECG/PPG/EEG/EDA/RSP/EMG/EOG; use when you need to clean, segment, and extract physiological features for HRV, event-related responses, complexity metrics, or multimodal psychophysiology pipelines.
devops37
nih-biosketch-builder
Generate NIH Biosketch documents compliant with the 2022 OMB-approved.
development37
pathml
A full-featured computational pathology toolkit for advanced WSI analysis, including multiplexed immunofluorescence (CODEX, Vectra), nuclei segmentation, tissue graph construction, and machine learning model training on pathology data. Supports over 160 slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
tools37
personal-statement
Use when writing medical school personal statements, residency application essays, fellowship statements, or graduate school admissions essays. Crafts compelling narratives highlighting clinical experiences, research achievements, and career motivations for healthcare education applications.
tools37
phylogenetic-tree-styler
Analyze data with `phylogenetic-tree-styler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
poster-layout-planner
Use poster layout planner for other workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
preclinical-pkpd-analyst
Use preclinical pkpd analyst for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
tools37
presentation-hook
Creates engaging opening statements and powerful closings for medical.
content-media37
prospero-registration-helper
Assists researchers in generating PROSPERO registration content for meta-analyses from a title and optional protocol. Use when the user wants to draft a PROSPERO registration form.
tools37
pseudotime-trajectory-viz
Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
pydeseq2
Differential gene expression analysis for bulk RNA-seq count matrices using a DESeq2-like workflow in Python; use when you need Wald tests, FDR correction, and optional LFC shrinkage for condition/batch/covariate designs.
development37
pydicom
A Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when you need to read, write, or modify DICOM format medical imaging data, extract pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymize DICOM files, process DICOM metadata and tags, convert DICOM images to other formats, handle compressed DICOM data, or work with medical imaging datasets. Suitable for tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
development37
quadas-c-assessment for diagnostic accuracy studies
Automated bias assessment for diagnostic accuracy studies using QUADAS-C criteria. Requires full text input.
tools37
quapas-quality-assessment for prognosis studies
Evaluates bias in medical literature (prognosis studies) using QUAPAS criteria. Use when the user wants to assess the quality or risk of bias of a medical paper text.
testing37
radiology-image-quiz
Use when creating radiology educational quizzes, preparing board exam questions, or studying medical imaging cases. Generates interactive quizzes with X-ray, CT, MRI, and ultrasound images for medical education.
content-media37
rebuttal-letter-strategist
Use rebuttal letter strategist for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
research-grants
Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan's NSTC when you need agency-compliant narratives, budgets, and review-criteria alignment for a specific solicitation/FOA/BAA.
testing37
research-proposal-generator
Generates a comprehensive research proposal design based on input literature, including hypothesis, mechanism verification, and budget. Use when the user wants to design a research project from a paper.
content-media37
response-letter
Helps organize reviewer comments and generate a standardized Word (.docx) response letter that maps each change to its exact location (page/paragraph/line). Use when revising a manuscript, replying to peer-review feedback, or preparing internal review responses.
documentation37
response-tone-polisher
Polishes response letters by transforming defensive or harsh language.
tools37
rowan
Cloud-based quantum chemistry platform providing a Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformational search, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Suitable for tasks involving quantum chemistry calculations, molecular property prediction, DFT or semi-empirical methods, neural network potentials (AIMNet2), protein-ligand binding prediction, or automated computational chemistry pipelines. Provides cloud computing resources without local installation.
development37
scikit-bio
A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard formats (FASTA/FASTQ/Newick/BIOM).
tools37
scvi-tools
Deep generative models for single-cell omics; use when you need probabilistic batch correction (scVI), transfer learning, uncertainty-aware differential expression, or multimodal integration (totalVI/MultiVI).
tools37
smiles-de-salter
Analyze data with `smiles-de-salter` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
spatial-transcriptomics-mapper
Map spatial transcriptomics data from 10x Genomics Visium/Xenium onto.
data-ai37
statistical-analysis
Guided statistical analysis for test selection, assumption checks, power analysis, and APA-style reporting. Use when you need to choose an appropriate statistical test for your data and produce publication-ready results (including effect sizes and diagnostics).
testing37
upset-plot-converter
Convert complex Venn diagrams with more than 4 sets to clearer Upset.
tools37
survival-curve-risk-table
Analyze data with `survival-curve-risk-table` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
table-1-generator
Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
tools37
tone-adjuster
Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting clinical notes for patient handouts. Maintains medical accuracy while adjusting readability level.
tools37
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).
development37
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.
tools37
drug-interaction-checker
Check for interactions between multiple medications, including severity classification and mechanism explanations.
testing37
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.
documentation37
ihc-if-optimizer
Optimize IHC/IF protocols for specific tissues and antigens
testing37
hmdb-database
Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.
tools37
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.
testing37
conference-poster-pitch
Use conference poster pitch for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
dicom-anonymizer
De-identify DICOM medical images by removing PHI tags for research sharing, with audit logging and study-linkage preservation support.
testing37
clinvar-database
Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.
tools37
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.
development37
wb-troubleshooter
Western Blot troubleshooting guide with step-by-step solutions
documentation37
serial-dilution-calculator
Generate qPCR/ELISA dilution protocols with precise pipetting steps
testing37
mouse-colony-planner
Calculate breeding timelines and cage requirements for transgenic mouse colonies
tools37
multi-omics-integration-strategist
Design multi-omics integration strategies for transcriptomics, proteomics, and metabolomics data analysis
data-ai37
flow-panel-designer
Design multicolor flow cytometry panels minimizing spectral overlap
content-media37
hypothesis-generation
Structured scientific hypothesis formulation from observations; use when you have experimental observations or preliminary data and need testable hypotheses with predictions, mechanisms, and validation experiments.
testing37
waste-disposal-guide
Guide for disposing specific chemical wastes into the correct colored waste containers, with safety precautions and regulatory compliance notes.
testing37
arrive-guideline-architect
Generate ARRIVE 2.0 compliant animal research protocols with structured experimental design, sample size calculations, and reporting checklists. Ensures transparency, reproducibility, and ethical compliance in in vivo studies.
testing37
time-zone-planner
Plan cross-time-zone meeting windows for distributed teams, providing region-by-region local time mappings and tradeoff analysis for scheduling decisions.
testing37
treatment-plans
Generate concise (typically 1–4 pages) patient-centered medical treatment plans in LaTeX/PDF when a clinician needs an actionable plan with SMART goals, evidence-based interventions, monitoring, and HIPAA-aware documentation.
tools37
uspto-database
Access USPTO data (Patent Search, PEDS, TSDR, assignments) when you need to query patents/trademarks and retrieve prosecution or status information programmatically.
development37
vector-text-fixer
Fix garbled text in PDF/SVG vector graphics caused by font encoding issues, making files editable in AI tools. Supports batch processing and JSON export for manual correction.
tools37
task-reminder
Organize scattered tasks into actionable lists and generate daily/weekly/deadline reminder plans when you need a structured schedule and exportable outputs (MD/CSV), with optional system notifications.
data-ai37
symptom-checker-triage
Suggest triage levels (Emergency, Urgent, Outpatient) based on red flag symptoms using a rule-based engine. For AI-assisted decision support only — not a substitute for professional medical diagnosis.
testing37
search pubmed
An intelligent tool for precision medical literature search using PubMed's E-utilities API.
tools37
shift-handover-summarizer
Generate structured shift handover summaries from EHR records, highlighting critical events, vital sign changes, and pending tasks for incoming clinical staff.
tools37
short-video-script-generator
Generate popular science short video scripts based on topic, duration, and style. Invoke when the user needs to create scripts for short science videos.
testing37
slide-deck-images
Generate professional slide-deck SVG images (not PPTX/PDF) when users ask to “create slides / slide deck / PPT” and need image outputs.
content-media37
sample-size-basic
Basic sample size calculator for clinical research planning with common statistical scenarios
tools37
science-popularization-article
Generates science popularization articles with titles and outlines based on medical topics and style preferences. Invoke when user needs to create medical/science popular content for public education.
testing37
pptx-posters
Generate PowerPoint presentations and academic posters from paper abstracts or full paper content, with automatic layout optimization and citation formatting.
development37
reagent-expiry-alert
Scan reagent barcodes or IDs, log expiration dates, and generate multi-level alerts before reagent expiry to support laboratory inventory management.
development37
reproducibility-check
Check whether a paper’s Methods section contains all information needed for replication; use when preparing a manuscript for submission or reviewing methodological completeness.
development37
resubmission-deadline-tracker
Track manuscript resubmission deadlines and automatically generate phase-appropriate task breakdowns for academic researchers based on remaining time.
data-ai37
plotly
Interactive visualization library for Python. Use it when you need hover tooltips, zoom/pan, selection, animations, or charts embeddable in web pages (e.g., dashboards, exploratory analysis, presentations).
tools37
poster-designer
Generate professional poster design concepts and optimized image-generation prompts, then automatically run a drawing script to produce the final poster image when a user needs a poster.
data-ai37
PPTX Skill
Create, edit, and extract content from PowerPoint (.pptx) files; use when you need to generate slides programmatically, update existing decks, or export slide previews.
content-media37
pdf-extract
Extract PDF selectable text and full-page or segmented page images (including tables) into Markdown with per-page headings and image links; use when you need both readable text and page visuals for PPT creation, review, or analysis.
content-media37
patient-consent-simplifier
Simplify informed consent documents into patient-friendly language while maintaining regulatory compliance (FDA 21CFR50, ICH-GCP, HIPAA) and required legal elements.
devops37
mindmap
Generate mindmaps locally/offline with native HTML/CSS/JS (no external libraries); use when you need to parse Plain Text node structures or map LLM outputs into an on-device visualization.
development37
mnemonic-generator
Create memory aids for anatomy and pharmacology
data-ai37
multi-panel-figure-assembler
Assemble 6 sub-figures (A–F) into a high-resolution composite figure with consistent labels, padding, and publication-ready DPI.
tools37
multi-source-news-writer
Integrates multiple news sources into a single, cohesive press release using an inverted pyramid structure and AP style. Use when you have raw news content and a topic, and need a professional press release.
documentation37
meeting-assistant
Extracts key meeting information in chronological order and outputs decisions and action items; use when you need meeting minutes, action tracking, or project sync notes from transcripts or raw notes.
development37
meeting-minutes-generator
Generates structured meeting minutes from text transcripts. Use when the user provides text content and wants a structured summary with a signature.
content-media37
microscopy-scale-bar-adder
Add accurate, publication-ready scale bars to microscopy images given pixel-to-unit calibration data.
data-ai37
medical-case-report-generator
Generates a patient-friendly medical case report tweet from case images and disease name. Use when the user provides a medical case image and wants a structured report or tweet.
business37
markitdown
Convert files and Office documents into clean Markdown when you need LLM-friendly, token-efficient text (e.g., for summarization, search, RAG ingestion, or dataset preparation).
testing37
medical-case-interpreter
Generates compliant medical case report articles for WeChat.
business37
medical-unit-converter
Convert medical laboratory values between units (mg/dL to mmol/L, etc.) with formula transparency and clinical reference ranges. Supports glucose, cholesterol, creatinine, and hemoglobin conversions.
tools37
literature-management
Import local literature into a managed library; trigger when you need offline deduplication, tagging, and a searchable index.
development37
literatureimages-interpretation
Interpret figures in academic papers and their captions when the input is a PDF-to-Markdown document with page markers and image links, producing a structured Markdown report for extracting variables, trends, and conclusions.
testing37
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.
testing37
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.
testing37
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.
data-ai37
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.
data-ai37
image-duplication-detector
Detect image duplication and tampering in manuscript figures using computer vision algorithms
development37
image-processing
Batch-convert and compress local images with Pillow; use when you need an offline, scriptable pipeline for directory-based processing.
devops37
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.
development37
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.
tools37
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.
content-media37
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.
tools37
spreadsheet-ops
Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook recalculation.
development37
experimental-data-analysis
Perform statistical analysis on experimental data (descriptive stats, t-tests, ANOVA, multiple comparisons) when you need to interpret experimental results, assess statistical significance, or generate reproducible reports.
testing37
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.
development37
drug-pronunciation
Provides correct pronunciation guides for complex drug generic names. Generates phonetic transcriptions using IPA and audio generation markers for medical terminology.
testing37
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.
testing37
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.
testing37
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.
tools37
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.
testing37
conference-schedule-optimizer
Use when planning conference schedules, optimizing session selection at scientific meetings, managing time between presentations, or maximizing networking at academic conferences. Creates personalized schedules balancing learning, networking, and career development for medical and scientific conferences.
development37
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.
testing37
brainstorming
Creative exploration and brainstorming; use it when you need to clarify goals/constraints, explore multiple options, and converge on a direction before implementation.
development37
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.
testing37
benchling-integration
Integrate with the Benchling R&D platform when you need to programmatically manage registry entities, inventory, ELN entries, workflows, events, or data warehouse analytics via API/SDK.
development37
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.
development37
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.
development37
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.
development37
article-format-adjustment
Adjust academic paper formatting and convert between DOCX/LaTeX/Markdown when you need to meet a journal or school template requirement.
development37
adaptyv
Cloud laboratory platform for automated protein testing and validation; use when you have designed protein sequences and need wet-lab experimental validation (e.g., binding, expression, thermostability, enzyme activity) and API-based submission/status/result retrieval.
development37
zinc-database
Access the ZINC (230M+ purchasable compounds) database when you need to look up compounds by ZINC ID/SMILES, run similarity/analog searches, or download 3D ready-to-dock structures for virtual screening and drug discovery.
documentation37
variant-annotation
Query and annotate gene variants from ClinVar and dbSNP databases. \n\.
tools37
venue-templates
Venue-specific LaTeX templates, formatting requirements, and submission guidelines for journals, conferences, posters, and grants—use when a target venue imposes strict layout, page limits, anonymization, or agency compliance rules.
development37
scientific-skills/Evidence Insights/tcm-biomedical-research-strategist
--- name: tcm-biomedical-research-strategist description: Designs complete, rigorous research plans for medicinal plant / TCM molecular mechanism studies against diseases (colorectal cancer, liver cancer, diabetes, etc.). Use whenever a user provides a broad herbal medicine or network pharmacology research direction and wants it translated into a structured, executable, methodologically defensible study plan. Triggers: "research plan for herbal medicine", "network pharmacology study design", "TC
development37
translational-gap-analyzer
Assess translational gaps between preclinical models and human diseases.
tools37
uniprot-database
Direct REST API access to UniProt for protein search, entry retrieval, and identifier mapping; use when you need programmatic UniProtKB queries or cross-database ID conversion.
development37
target-novelty-scorer
Score the novelty of biological targets through literature mining and.
tools37
string-database
Access the STRING database to map identifiers, retrieve protein–protein interaction networks, and run functional/PPI enrichment when you need interaction context for a gene/protein set.
data-ai37
systematic-review-screener
Automated abstract screening tool for systematic literature reviews with PRISMA workflow support.
tools37
sds-msds-risk-scanner
Extract hazard codes and safety info from chemical safety datasheets.
development37
semantic-scholar-database
Access the Semantic Scholar Graph API to search papers and retrieve paper/author/citation data when you need literature discovery or citation graph exploration.
development37
scholar-evaluation
Implements the ScholarEval framework to evaluate scholarly documents; trigger when the user provides a PDF/DOCX/TXT file or pasted text and requests critique, scoring, or quality assessment.
development37
scientific-podcast-summary
Automatically summarize scientific podcasts like Huberman Lab and Nature.
testing37
scite-database
Access Scite.ai Smart Citations to classify how a paper is cited (supporting, contrasting, mentioning) and assess scientific claims; use it when you need to evaluate a paper’s reliability or its acceptance in the literature.
testing37
research-hotspot-analysis
Analyzes research hotspots and recommends literature based on a disease or topic. Use when the user wants to identify current research trends, hot topics, or get literature recommendations for a specific medical field or disease.
testing37
research-paper-downloader
Download academic papers from open-access sources when the user provides a DOI/arXiv ID or requests a keyword-based paper search, and return the saved PDF path.
content-media37
reagent-substitute-scout
Find validated alternative reagents based on literature citation data.
testing37
reference-finder
Automatically finds and ranks PubMed references for each sentence in scientific text; use when you need titles, DOIs, and brief recommendation reasons from the PubMed E-utilities API.
development37
reference-search
Multi-database literature search and search-strategy design that outputs structured, reproducible result lists; use when you need reference retrieval, systematic searching, review topic selection, or to construct a traceable search strategy.
testing37
rare-disease-hpo-mapper
Map patient symptoms to Human Phenotype Ontology terms for gene diagnosis.
tools37
phenotype-introduction
Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in Chinese academic writing.
data-ai37
plagiarism-checker-pre-screener
Use when: User provides text/document and asks to check originality, detect plagiarism, assess similarity, or rewrite high-duplicate content. Triggers: "check plagiarism", "originality check", "similarity detection", "改写重复内容", "降重", "查重", "原创性检测", "抄袭检查" Input: Text content or document (txt, md, docx support via text extraction) Output: Originality score, highlighted duplicate/similar paragraphs, paraphrasing suggestions
research37
patent-landscape
Use when analyzing biotech patent landscapes, identifying white spaces in pharmaceutical IP, tracking competitor patents, or assessing freedom to operate for drug development. Provides comprehensive patent analysis and strategic insights for life sciences innovation.
development37
open-access-scout
Use when finding open access journals, checking journal policies, or identifying predatory publishers. Helps researchers locate legitimate open access venues and avoid publication scams.
testing37
literature-experiment-extract
Extract experimental models, experimental methods, and biomarker information from paper Markdown (typically produced by PDF-to-Markdown tools) when a user provides paper Markdown and needs a structured, evidence-backed summary (1 Markdown + 3 CSVs).
tools37
literature-filtering
Filter literature by publication year, journal, and predefined screening rules to produce inclusion/exclusion lists; use when conducting preliminary screening or systematic review screening to narrow the literature scope.
tools37
gget
Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or keywords.
tools37
fda-guideline-search
Search FDA industry guidelines by therapeutic area or topic.
documentation37
ensembl-database
Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.
development37
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.
development37
ena-database
Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.
development37
ecrf-designer
Design clinical trial CRFs with proper validation rules
tools37
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.
development37
competitor-trial-monitor
Monitor competitor clinical trial progress and alert on market risks.
tools37
concept-explainer
Uses analogies to explain complex medical concepts in accessible terms.
data-ai37
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB) when you need to query gene-drug interactions, CPIC guidelines, allele functions, and drug-label PGx content for precision medicine and genotype-guided dosing.
tools37
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.
testing37
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.
development37
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).
development37
biorxiv-database
Search, retrieve metadata, and download PDFs for bioRxiv preprints; use when you need to discover biology preprints by keywords/authors/date ranges and programmatically fetch their details.
data-ai37
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.
tools37
volcano-plot-labeler
Analyze data with `volcano-plot-labeler` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
table-1-generator
Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
tools37
study-design-scale-selector
Determines the appropriate Risk of Bias assessment scale for a medical study based on its design (RCT, Cohort, etc.), using PubMed metadata lookup or text analysis. Use when the user wants to know which quality assessment tool to use for a specific paper (given PMID or abstract).
tools37
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.
development37
seaborn
Statistical visualization library integrated with pandas; use it when you need fast EDA of distributions, relationships, and categorical comparisons (e.g., box/violin/pair plots and heatmaps) with strong default aesthetics on top of matplotlib.
development37
scanpy
Standard single-cell RNA-seq analysis pipeline. For quality control (QC), normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression analysis, and visualization. Best suited for exploratory single-cell transcriptomics analysis using established workflows. For deep learning models, use scvi-tools; for data format issues, use anndata.
tools37
quality-assessment
Automates critical appraisal and quality assessment for research papers by analyzing text against established methodological standards (such as risk of bias tools, quality checklists, or reporting guidelines) and synthesizing a structured evaluation report. Use when you need to assess the methodological quality, internal validity, or reporting completeness of any type of study—including RCTs, observational studies, systematic reviews, qualitative research, or diagnostic accuracy studies.
tools37
pyopenms-skill
Comprehensive tool for computational mass spectrometry using PyOpenMS; use when you need to read/write MS formats (mzML/mzXML/MGF), run signal processing (smoothing/peak picking), detect isotope features, or perform peptide identification in proteomics/metabolomics workflows.
tools37
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.
tools37
neoantigen-predictor
Predict neoantigens that may be recognized by the immune system based.
tools37
meta-radial-plot
Generate radial plots (Radial Plot/Galbraith Plot) for heterogeneity analysis. Visually assess heterogeneity across studies by displaying the relationship between standardized effect sizes and precision. Input: Meta-analysis data in CSV format; Output: Radial plot PNG and data CSV.
development37
meta-abstract-screener
Screens research papers based on title/abstract and inclusion criteria, providing a structured Yes/No/Maybe decision. Use when you need to filter literature for meta-analysis or systematic reviews.
testing37
meta-baujat-plot
Generate Baujat plots for heterogeneity analysis. Identify studies that contribute most to the overall meta-analysis results and heterogeneity, helping discover potential outlier studies. Input meta-analysis data CSV, output Baujat plot PNG and contribution data CSV.
data-ai37
matplotlib
A low-level plotting library for comprehensive customization. Use when fine-grained control over every plot element is needed, creating new types of charts, or integrating into specific scientific workflows. Can export to PNG/PDF/SVG for publication. For quick statistical charts, use seaborn; for interactive charts, use plotly; for journal-style, publication-ready multi-panel charts, use scientific-visualization.
development37
geopandas
A Python library for reading, writing, and analyzing geospatial vector data; use it when you need spatial operations (buffer/overlay/join), CRS reprojection, or map visualization on formats like Shapefile/GeoJSON/GeoPackage or PostGIS.
development37
eln-template-creator
Generate standardized experiment templates for Electronic Laboratory Notebooks
tools37
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.
testing37
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.
testing37
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.
tools37
anndata
Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.
data-ai37
TorchDrug (English)
PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, and retrosynthesis. If you need pretrained models and diverse feature extractors, use deepchem; if you need benchmark datasets, use pytdc.
development37
sample-size-power-calculator
Advanced sample size and power calculations for complex study designs including survival analysis, clustered designs, and multiple comparisons.
content-media37
recommendation-letter-assistant
Helps faculty and mentors draft standardized recommendation letters for.
tools37
referral-letter-generator
Generate medical referral letters with patient summary, reason for referral.
tools37
prior-auth-letter-drafter
Generate professional prior authorization request letters for insurance companies with proper clinical justification and formatting.
tools37
peer-review-response-drafter
Assist in drafting professional peer review response letters. Trigger.
tools37
networking-email-drafter
Draft professional follow-up emails to contacts made at conferences - not too pushy, but memorable.
data-ai37
meeting-minutes
Use meeting minutes for other workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
mentorship-meeting-agenda
Generate structured agendas for mentor-student one-on-one meetings
tools37
medical-device-mdr-auditor
Audit medical device technical files against EU MDR 2017/745 regulations.
development37
labarchive-integration
Converts LabArchives notebook data, entry metadata, and authorized ELN exports into manuscript-ready academic writing outputs such as Methods sections, data-availability statements, reproducibility appendices, experiment timelines, and submission support notes. Optional bundled scripts can be used to collect or validate source notebook data before writing.
testing37
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.
development37
data-management-plan-creator
Automatically generate NIH 2023-compliant Data Management and Sharing Plan (DMSP) drafts following FAIR principles
testing37
meta-results-funnel-plot-generator
Generates a Meta-analysis results section description for funnel plots, including statistical tables (Egger's, Begg's, Trim & Fill) and figure legends. Supports English and Chinese outputs. Use when user provides a funnel plot image and statistics and wants a formatted report.
development37
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.
documentation37
outcome-extraction for clinical trials
Clinical research outcome extraction for meta-analysis. Use when users need to extract outcome measures (binary, continuous, or survival data) from clinical research papers for systematic review and meta-analysis. Handles both database lookup by PMID and real-time LLM extraction.
tools37
paper-tweet-generator
Generates a structured reading tweet from an academic paper (PDF, Word, or Text), highlighting specific product advantages. Use when the user wants to turn a document into a social media post or reading summary.
testing37
postdoc-fellowship-matcher
Filter and match postdoctoral fellowship opportunities based on applicant nationality, years since PhD, and research field from a curated database.
documentation37
meta-results-forest-plot-analyzer
Analyzes forest plots for meta-analysis, generating detailed descriptions and formatting figure legends in Chinese or English. Use when the user wants to interpret a forest plot image, describe its statistical significance (heterogeneity, p-value), and format the output with specific figure legends.
development37
unstructured-medical-text-miner
Mine unstructured clinical text from MIMIC-IV to extract diagnostic logic.
tools37
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.).
tools37
etetoolkit
ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.
tools37
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.
development37
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.
testing37
word-read-write
Create and read Microsoft Word (.docx) documents. Use this skill when you need to generate reports/letters/templates as .docx or extract readable text from existing .docx files.
documentation37
rct-bias-assessment-rob2
Automates Risk of Bias 2 (ROB2) assessment for RCT papers by analyzing text against specific domains and synthesizing a report. Use when you need to assess the quality of a clinical trial paper or evaluate risk of bias.
tools37
journal-club-presenter
Generate journal club slides with background, critique, and discussion.
tools37
hgnc-api
Access the HGNC (HUGO Gene Nomenclature Committee) database to search for and retrieve gene information including symbols, names, IDs, and other metadata.
development37
gwas-database
Query the NHGRI-EBI GWAS Catalog to retrieve SNP–trait associations, study metadata, and (when available) summary statistics when you need evidence for a variant, trait/disease, gene, or genomic region.
testing37
freezer-sample-locator
Track and retrieve sample locations in -80°C freezers with hierarchical storage organization. Trigger conditions: - User needs to record sample storage positions (freezer ID, level, rack, box, grid position) - User requests to search samples by name, project, date, or location - User requires sample inventory management and export functionality Input: Sample metadata (name, project, quantity) and storage coordinates Output: Structured sample location records with search and export capabilities Success criteria: - Accurate position recording without conflicts - Fast search and retrieval (<1 second for 1000+ samples) - Data integrity maintained across operations - Export in multiple formats (JSON, CSV) Risk level: MEDIUM (Script execution with file system access) Technical difficulty: INTERMEDIATE Version: v1.0 Owner: 研发部 Last updated: 2026-02-06
development37
metagenomic-krona-chart
Analyze data with `metagenomic-krona-chart` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
primer-design-check
Check primers for dimers, hairpins, and off-target amplification
testing37
meta-forest-continuous-plot
Generate forest plots for meta-analysis of continuous data. Input a CSV file containing study names, means, standard deviations, and sample sizes for experimental and control groups. Output forest plot PNG and data table CSV.
development37
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.
development37
citation-management
Comprehensive citation management for academic research; use when you need to discover papers (Google Scholar/PubMed), extract/verify metadata (DOI/PMID/arXiv/URL), and produce validated, clean BibTeX for manuscripts.
development37
interview-mock-partner
Simulates behavioral interview questions for medical professionals.
tools37
meta-title-generator
Generates Meta-Analysis research titles based on user keywords, utilizing PubMed search results if available, or creative generation otherwise. Use when the user wants to brainstorm or generate titles for a meta-analysis, specifically starting from keywords or a topic.
testing37
kol-profiler
Analyze physician academic influence and collaboration networks
testing37
protocol-deviation-classifier
Determine whether an incident in a clinical trial is a "major deviation.
tools37
visual-content-desc
Generates detailed text descriptions of medical images and charts for.
data-ai37
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)
development37
outlier-detection-handler
Use outlier detection handler for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
bio-ontology-mapper
Map unstructured biomedical text to standardized ontologies (SNOMED CT.
tools37
abstract-summarizer
Transform lengthy academic papers into concise, structured 250-word abstracts.
testing37
scientific-skills/Protocol Design/non-tumor-ml-research-planner
--- name: non-tumor-ml-research-planner description: Generates complete non-tumor biomedical machine learning research designs from a user-provided research direction. Always use this skill when users want to plan bioinformatics + ML papers for non-cancer diseases (metabolic, cardiovascular, kidney, inflammatory, autoimmune, infectious, neurological, endocrine, wound healing, chronic multifactor), design diagnostic biomarker studies, combine GEO datasets with feature selection and ML modeling, o
development37
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.
tools37
scikit-survival
A comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival; use it when you need to model censored time-to-event outcomes, fit Cox/RSF/GB models or Survival SVMs, evaluate with C-index/Brier score, or handle competing risks.
tools37
scientific-skills/Protocol Design/two-sample-mr-research-planner
--- name: two-sample-mr-research-planner description: Generates complete two-sample Mendelian randomization (MR) research designs from a user-provided research direction. Use when users want to design, plan, or build a study using two-sample MR to test causal relationships. Triggers: "design a two-sample MR study", "build a publishable MR paper", "test whether this biomarker causally affects this disease", "generate Lite/Standard/Advanced MR plans", "screen multiple exposures with MR", "bidirect
development37
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.
development37
spreadsheet-ops
Spreadsheet processing and analysis for CSV/Excel; trigger when users ask to merge/clean tabular data, run statistics, add/edit Excel formulas, apply formatting, generate charts, or force workbook recalculation.
development37
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.
testing37
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.
development37
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.
development37
keyword-velocity-tracker
Calculate literature growth velocity and acceleration to assess research.
testing37
digital-twin-patient-builder
Build digital twin patient models to test drug efficacy and toxicity in virtual environments
development37
sequence-alignment
A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.
development37
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.
data-ai37
patent-assistant
Assists R&D teams with patent technical disclosure drafting and patent/novelty search analysis; use when users ask to write a patent disclosure, structure an invention description, search related patents, or assess novelty.
documentation37
reactome-skill
Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.
development37
meta-search-builder
Medical literature search strategy generator. Given a user's natural-language description (e.g., meta-analysis topic, PICOS elements, research question), automatically extract medical entities (disease, intervention, population, outcomes) and generate professional search queries for seven major databases (PubMed, Cochrane, Embase, Web of Science, CNKI, Wanfang, VIP). Useful for developing search strategies for systematic reviews and meta-analyses.
development37
soft-article-writer
Generates high-quality promotional soft articles with structured outlines, tailored introductions, and optimized titles based on product info and hot topics. Use when you need to write promotional content, "soft articles" (), or marketing copy that integrates product highlights with current trends, news, or industry insights.
testing37
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.
tools37
pdf-ppt
Create literature-report PPTX decks from PDF papers. Use when you must extract a paper’s metadata, summarize the study, interpret Results/Figures/Tables, and generate slides with 1:1 figure-to-text alignment and layout rules (triggered by requests like “PDF to PPT”, “literature report slides”, or “turn this paper into a presentation”).
data-ai37
flow-cytometry-gating-strategist
Recommend optimal flow cytometry gating strategies for specific cell types and fluorophores
testing37
3d-molecule-ray-tracer
Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.
tools37
meta-forest-model-plot
Generate forest plots for meta-analysis of survival data. Input is a CSV file containing study names, HR and 95% confidence intervals, output forest plot PNG and data table CSV. Supports both R and Python scripts.
development37
grant-proposal-assistant
Grant proposal writing assistant for NIH (R01/R21), NSF and other mainstream funding applications. Triggers when user needs help writing specific aims, research strategy, budget justification, or other grant sections. Provides templates, section generators, and best practice guidance for competitive grant proposals.
testing37
dashboard-design-for-trials
Design dashboard layout sketches for clinical trials showing enrollment progress and adverse event rates
tools37
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.
development37
plan-generator
Automatically generates a Markdown final-exam review plan or lab experiment schedule when you provide a date range, tasks/items, and available daily hours (via interactive prompts or a one-time JSON input).
data-ai37
reference-style-sync
One-click synchronization and standardization of reference formats in literature management tools, intelligently fixing metadata errors.
tools37
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.
development37
pysam
Genomic file toolkit. For reading/writing SAM/BAM/CRAM alignment files, VCF/BCF variant files, FASTA/FASTQ sequences, extracting regions, calculating coverage, suitable for NGS data processing pipelines.
tools37
pdb-database
Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.
data-ai37
meta-rob2-plot
Draw ROB2 risk-of-bias plots, including a Traffic Light Plot and a Summary Bar Plot. Input is a CSV file with ROB2 assessments for each study; output are two PNG plot files.
research37
q-and-a-prep-partner
Predict challenging questions for presentations and prepare structured responses.
content-media37
peer-review
Conduct professional peer reviews for papers or theses, providing structured evaluations and improvement suggestions; use when you need a pre-submission assessment, an internal review, or academic quality control.
testing37
semantic-consistency-auditor
Use semantic consistency auditor for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
medical-research-literature-reader-pro
A medical-research-native literature reading skill for users with clinical, bioinformatics, translational, and basic experimental backgrounds. Use this skill whenever a user wants to read, analyze, critique, or interpret a medical or scientific paper — whether they provide a PDF, abstract, DOI, PMID, or just a title. Triggers include requests like "analyze this paper", "critique this study", "is this a strong paper?", "give me similar studies", "prepare me for journal club", "help me understand this bioinformatics paper", "what are the weaknesses here?", or "turn this into a mind map". Also activate for any downstream deliverables such as journal club kits, comparison tables, PI decision briefs, replication starters, or follow-up experiment designs. Do NOT treat as a generic summarizer — this skill performs structured evidence-type classification, track-specific critical appraisal, interpretation-boundary judgment, and research-grade follow-up generation.
tools37
open-source-license-check
Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).
development37
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.
testing37
scientific-skills/Protocol Design/network-tox-docking-research-planner
--- name: network-tox-docking-research-planner description: Generates complete network toxicology + molecular docking research designs from a user-provided toxicant and disease/phenotype. Always use this skill when users want to investigate how an environmental toxicant, endocrine disruptor, heavy metal, food contaminant, pharmaceutical residue, or consumer product chemical may contribute to a disease through shared molecular targets, hub genes, pathways, and docking evidence. Trigger for: "netw
testing37
sci-paper-reviewer
Simulates a strict SCI peer-review workflow; trigger when a user uploads or pastes a manuscript (PDF/DOC/DOCX/TXT) and requests an innovation score (1–12) plus experimental-logic vulnerability checks and revision suggestions.
testing37
pdf-extract
Extract PDF selectable text and full-page or segmented page images (including tables) into Markdown with per-page headings and image links; use when you need both readable text and page visuals for PPT creation, review, or analysis.
content-media37
schedule-management
Local schedule management for adding events, tracking deadlines, generating reminders, and detecting time conflicts when users need offline scheduling with optional popup notifications.
tools37
study-limitations-drafter
Use study limitations drafter for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
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.
tools37
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.
development37
method-writing
Write and revise the Methods section of research papers to ensure reproducibility; use when preparing an IMRAD manuscript or responding to journal/reporting-guideline requirements (e.g., CONSORT/STROBE/PRISMA).
testing37
grant-budget-justification
Use grant budget justification for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
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.
testing37
meta-screening-fulltext
Screen full-text papers against inclusion/exclusion criteria, with optional PubMed metadata check using PMID. Use when the user needs to evaluate a paper for a meta-analysis.
testing37
variant-pathogenicity-predictor
Integrate REVEL, CADD, PolyPhen scores to predict variant pathogenicity.
testing37
scrna-cell-type-annotator
Auto-annotate cell clusters from single-cell RNA data using marker genes.
data-ai37
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.
development37
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.
development37
statistical-analysis-advisor
Recommends appropriate statistical methods (T-test vs ANOVA, etc.) based.
testing37
esm
Toolkit for protein language models (ESM3 for multimodal generative protein design; ESM C for efficient embeddings). Use when you need sequence/structure/function generation or prediction, inverse folding, protein embeddings, or scalable inference via local weights or the Forge API.
tools37
toxicity-structure-alert
Analyze data with `toxicity-structure-alert` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.
testing37
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.
development37
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.
development37
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.
tools37
pathology-roi-selector
Use pathology roi selector for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
meta-criteria-generator
Generates scientifically sound inclusion and exclusion criteria for Meta-Analysis based on a given title or keywords. Use when user wants to design eligibility criteria for a systematic review or meta-analysis.
testing37
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.
development37
molecular-review-workflow
Generates academic reviews for molecules in diseases using PubMed research. Invoke when user needs biomedical literature review with Vancouver citation format.
development37
arboreto
Infer gene regulatory networks (GRNs) from gene expression matrices using GRNBoost2 or GENIE3; use when analyzing bulk or single-cell RNA-seq to identify TF→target regulatory relationships.
tools37
medication-adherence-message-gen
Use medication adherence message gen for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
lamindb
This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
development37
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.
development37
protocol-standardization
Standardize fragmented experimental steps into reproducible protocol documents when you need method organization, lab SOP drafting, or cross-operator reproducibility; missing parameters must be explicitly marked as "To be supplemented/Not provided".
testing37
comparison-table-gen
Auto-generates comparison tables for concepts, drugs, or study results.
research37
lipinski-rule-filter
Filter compound libraries based on Lipinski's Rule of Five for drug-likeness.
tools37
patient-recruitment-ad-gen
Generate ethical, compliant, and patient-friendly recruitment advertisements for clinical trials.
tools37
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.
research37
market-research-report-generator
Generates professional market research reports by analyzing business intent, decision levels, and conducting multi-source data retrieval (Web, PubMed, Clinical Trials).
tools37
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.
tools37
deeptools
NGS analysis toolkit. Used for BAM to bigWig conversion, quality control (correlation, PCA, fingerprint plots), heatmaps/feature plots (TSS, peaks), suitable for ChIP-seq, RNA-seq, ATAC-seq visualization.
tools37
voice-to-protocol-transcriber
Record experimental procedures and observations via voice commands during lab work. Real-time transcription for structured experiment documentation.
documentation37
result-figure-consistencycheck
Checks consistency between paper result descriptions and figure legends (text-only) when the input is a PDF-to-Markdown full text containing page breaks (e.g., `## Page XX`) and legend text; outputs a Markdown consistency report and a UTF-8 CSV issue list.
testing37
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.
development37
smart-journal-monitor
Use smart journal monitor for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
image-ocr
Extract text from images with Tesseract OCR; use it when you need to recognize text from PNG/JPEG/TIFF/BMP images, select a language model, or run OCR via natural-language requests (e.g., "Interpret the image at C:\path\image.png").
data-ai37
scientific-skills/Protocol Design/faers-multi-drug-soc-planner
--- name: faers-multi-drug-soc-planner description: 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 neurop
testing37
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.
testing37
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.
documentation37
anatomy-quiz-master
Generate interactive anatomy quizzes for medical education with multiple.
tools37
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.
documentation37
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.
testing37
cover-letter-drafter
Generates professional cover letters for journal submissions and job.
tools37
ectd-xml-compiler
Automatically convert uploaded drug application documents (Word/PDF) into XML skeleton structure compliant with eCTD 4.0/3.2.2 specifications.
development37
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.
testing37
latex-posters
Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter. Use when a user needs poster-ready section copy, figure plans, captions, and package-specific layout decisions for conference or thesis posters.
testing37
medical-scribe-dictation
Convert physician verbal dictation into structured SOAP notes. Trigger.
testing37
meta-results-sensitivity-analysis
Generates the "Results" section for meta-analysis sensitivity analysis based on statistical tables and titles. Use when the user wants to describe sensitivity analysis results or format sensitivity tables for a meta-analysis paper.
development37
paper-2-web
Use this skill when converting academic papers to promotional and presentation formats, including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). This skill is suitable for paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing printable posters from LaTeX or PDF source.
development37
q-and-a-prep-partner
Predict challenging questions for presentations and prepare responses
content-media37
residency-interview-prep
Mock interview preparation tool for residency Match interviews. Generates.
tools37
usmle-case-generator
Generate USMLE Step 1/2 style clinical cases with patient history, physical.
tools37
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.
development37
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.
development37
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.
testing37
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.
development37
facs-gating-viz-style
Use facs gating viz style for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
gene-structure-mapper
Use gene structure mapper for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
imaging-data-commons
Use idc-index to query and download public cancer imaging data from NCI Imaging Data Commons. Used to access large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Supports metadata querying, in-browser visualization, and license checking.
testing37
in-silico-perturbation-oracle
Virtual gene knockout simulation using foundation models to predict transcriptional changes
data-ai37
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.
testing37
meta-forest-binary-plot
Generate meta-analysis forest plots for binary classification data. Input is a CSV file containing study names, event counts and sample sizes for experimental and control groups. Output includes forest plot PNG and data table CSV.
data-ai37
meta-picos-generator
Generates PI(E)COS structure (Population, Intervention, Comparator, Outcomes, Study Design) from Meta-analysis or study titles. Use when the user wants to extract these elements from a title.
content-media37
meta-sensitivity-plot
Generate leave-one-out sensitivity analysis plots for meta-analysis. Input is a CSV file containing meta-analysis data; outputs are a sensitivity forest plot (PNG) and a sensitivity data table (CSV) showing pooled effect estimates after excluding each study in turn.
data-ai37
probast-quality-assessment for prediction model studies
Assess bias in medical prediction model studies using PROBAST tool. Use when user wants to evaluate the quality or risk of bias of a medical paper (text or PDF).
tools37
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.
testing37
sanger-chromatogram-qa
Use sanger chromatogram qa for data analysis workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
singlecell-portal
Programmatically query public single-cell study metadata from the Broad Institute Single Cell Portal REST API when you need to search and filter datasets by organism, tissue, disease, or cell type without an API key.
development37
survival-analysis-km
Kaplan-Meier survival analysis tool for clinical and biological research. Generates publication-ready survival curves with statistical tests.
tools37
synthetic-bio-circuit-designer
Design gene circuits for synthetic biology applications
testing37
western-blot-quantifier
Automatically identify Western Blot gel bands, perform densitometric analysis, and calculate normalized values relative to loading controls.
research37
acronym-unpacker
Intelligent medical abbreviation disambiguation tool that resolves ambiguous acronyms using clinical context, specialty-specific knowledge, and document-level semantic analysis.
tools37
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.
testing37
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.
development37
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.
data-ai37
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.
development37
brenda-database
Programmatic access to the BRENDA enzyme database via the SOAP API; use when you need kinetic constants (Km, kcat, Vmax), reaction equations, enzyme properties (pH/temperature optima, stability), or enzyme discovery by EC/substrate/product.
development37
cellxgene-census
Programmatically query the CZ CELLxGENE Census (61M+ cells) when you need cross-tissue, disease, or cell-type expression data for population-scale queries and reference atlas comparisons.
data-ai37
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.
development37
clinicaltrials-gov-parser
Monitor and summarize competitor clinical trial status changes from ClinicalTrials.gov.
tools37
cosmic-database
Access COSMIC to download mutation datasets, query Cancer Gene Census, and retrieve mutational signatures when your genomic analysis requires curated somatic mutation resources.
data-ai37
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.
development37
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.
development37
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.
documentation37
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.
data-ai37
fda-database
Query the openFDA API to retrieve FDA regulatory datasets (drugs, devices, adverse events, recalls, submissions, UNII) when you need programmatic safety/regulatory evidence for analysis or research.
development37
funding-trend-forecaster
Analyze funding abstracts and project metadata to identify topic shifts and forecast near-term grant priorities.
data-ai37
gene-database
Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.
development37
grant-funding-scout
NIH funding trend analysis to identify high-priority research areas.
research37
grant-gantt-chart-gen
Use grant gantt chart gen for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.
testing37
ib-summarizer
Summarize core safety information from Investigator's Brochures for clinical.
tools37
icd10-cpt-coding-assistant
Automatically recommend ICD-10 diagnosis codes and CPT procedure codes from clinical notes. Trigger when: user provides clinical notes, patient encounter summaries, discharge summaries, or asks for medical coding assistance. Use for healthcare providers, medical coders, and billing professionals who need accurate code recommendations.
tools37
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.
development37
journal-impact-factor-trend
Show journal impact factor and quartile trends over 5 years.
tools37
journal-matchmaker
Analyzes academic paper abstracts to recommend optimal journals for submission, considering impact factors, scope alignment, and domain expertise.
data-ai37
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.
development37
kegg-database
Direct access to KEGG via the REST API for academic-only pathway/gene/compound/drug queries; use when you need precise HTTP-level control or targeted KEGG ID mapping.
development37
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.
testing37
scientific-skills/Evidence Insights/literature-extensive-read
--- name: literature-extensive-read description: Rapidly skim and summarize academic papers (default: PDF-to-Markdown full text with `## Page XX` pagination and image references) and output a structured extensive-reading summary in Markdown when you need to quickly understand research questions, methods, key results, conclusions, and decide whether intensive reading is worthwhile. license: MIT skill-author: AIPOCH --- ## When to Use - You have a paper converted from PDF to Markdown an
development37
low-resource-ai-researcher
Train high-performance medical LLMs on consumer GPUs using parameter-efficient fine-tuning
research37
medchem
Medicinal chemistry screening filters for compound prioritization; use when you need to apply drug-likeness rules, PAINS/structural alerts, and complexity metrics to triage or optimize libraries.
testing37
mr-scrna-research-planner
Generates complete Mendelian Randomization + single-cell transcriptomics (scRNA-seq) research designs from a user-provided direction. Always use this skill whenever a user wants to design, plan, or build a study combining MR and single-cell data — even if phrased as "help me write a paper on X", "design a bioinformatics study for Y", or "I want to study Z using MR and scRNA". Covers five study patterns (mechanism gene-set, key-cell, candidate-gene reverse validation, exposure-disease-cell triangulation, translational biomarker) 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, and publication upgrade path.
development37
open-targets-db
Query the Open Targets Platform to retrieve targets, diseases, or evidence records when you need target-disease association data and evidence-based scores for therapeutic discovery.
testing37