「reproducibility」の検索結果

This skill covers reproducible research pipelines and replication packages. Use when the user is setting up a research project directory structure, configuring workflow managers (Make, Snakemake, DVC), managing computational environments, preparing replication packages for journal submission, or debugging reproducibility failures. Triggers on "reproducible", "replication package", "Makefile", "Snakemake", "DVC", "pipeline", "workflow manager", "data versioning", "conda environment", "Docker", "seed management", "AEA data editor", "replication", "project structure", or "submission checklist".

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Run the R code review protocol on R scripts. Checks code quality, reproducibility, domain correctness, and professional standards. Produces a report without editing files. Make sure to use this skill whenever the user wants their existing R code evaluated or audited — not when they want new analysis written. Triggers include: "review my R script", "check my R code", "is my code replication-ready", "audit this R file", "does this code follow conventions", "will this reproduce", "check my analysis script", "code review", "review-r", or when the user has an existing .R file and wants quality feedback rather than new code.

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Build and verify replication packages — routes to reproducibility-auditor agent

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Review research code for reproducibility and quality, extract the paper's main empirical claims, compare paper to code, and write a constructive markdown report. Designed for social science / economics projects with LaTeX papers and Stata, R, or Python code.

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Integrate AI tools into economic research, teaching, and policy analysis with attention to privacy and reproducibility.

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Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

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Write research/technical reports with strong structure + figure standards. Supports Markdown/HTML/PDF outputs (Quarto optional), executive summary, methods, results, discussion, and reproducibility appendix.

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This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

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Exports sanitized metadata, parameters, reproducibility details, quality metrics, and optional review artifacts from Medical AI inference runs or evidence packs to MLflow. Use after inference, including NV-Generate runs; not for live training tracking, model registration, or clinical use.

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Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.

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ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

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Prepare evidence-bounded, constructive peer-review drafts and structured manuscript assessments. Use for authorized review of scientific manuscripts, protocols, preprints, or research proposals; reporting-guideline selection; claim–evidence checks; methods, statistics, reproducibility, ethics, figure/table, and citation critique; or revision-response planning.

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Standards and audits for writing academic papers, especially ML/NLP submissions to NeurIPS, ICML, ICLR, ACL, EMNLP, NAACL. Covers the author's house prose rules (zero em dashes, zero fluff, every sentence earns its place), verification of hallucinated claims and hallucinated or malformed bibliography entries, the ACL policy on AI writing assistance and what must be disclosed, and best practices for paper structure, experiments, reproducibility checklists, and rebuttals. Use this skill whenever the user is drafting, editing, polishing, restructuring, or reviewing a paper, abstract, intro, related work, rebuttal, or camera-ready; whenever they ask to "clean up" or "tighten" academic writing; whenever citations or a .bib file need checking; and whenever they ask what has to be disclosed about AI assistance. Reach for it even when the user only says "make this section better", "check my references", or "is this ready to submit".

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Build safe, local, defensive reproductions of ALREADY-PATCHED, publicly disclosed security vulnerabilities (CVEs, vendor advisories, AI-agent incidents) for whitepapers, control testing, and education. Use this skill whenever the user wants to reproduce, demonstrate, or write up a known vulnerability or security incident — phrases like "reproduce this CVE", "build a repro for", "demonstrate the EchoLeak/Cursor/postmark-mcp issue", "show how this exploit worked", "add a reproducibility guide", or "pull the NVD/CVE details for". It fetches advisory metadata from NVD and CVE.org, confirms the issue is fixed, and produces a vulnerable-vs-patched harness that is offline, loopback-only, and uses synthetic markers. It NEVER discovers, develops, or weaponizes new zero-days and refuses any unpatched or live-target request.

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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.

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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).

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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.

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

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

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Enforce the replication-protocol.md rule by cross-checking numeric claims in a manuscript against the actual R / Stata / Python outputs. Report PASS/FAIL per claim against tolerance thresholds. Use before submission and before releasing a replication package.

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Comprehensive manuscript review with three modes: single-pass (default), --adversarial critic-fixer loop, and --peer [journal] simulated peer-review pipeline (editor + 2 dispositioned referees + editorial decision, calibrated to a target journal). R&R continuation via --peer --r2/--r3; hostile-editor stress test via --peer --stress; reviewer-disposition variance reporting via --peer --variance N. Auto-invokes /review-r + /audit-reproducibility on referenced scripts unless --no-cross-artifact.

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Assemble a submission-ready replication package to the AEA Data and Code Availability Standard (DCAS) / openICPSR / Social Science Reproduction Platform expectations — standard replication README, dataset manifest, computational-requirements capture, a Table/Figure → script:line map, and a confidential-data deposit plan. Use when user says "build the replication package", "prepare the openICPSR deposit", "make the AEA data and code package", "DCAS compliance", "assemble the deposit for the journal", or after a paper is accepted and the journal's data editor needs the package. NOT a numeric verifier — it calls /audit-reproducibility to confirm claims reproduce before packaging.

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Machine learning experimentation reference for model-experimentation conventions, experiment tracking and reproducibility, dataset and model abstractions, ML engagement fundamentals, and model-production readiness. Use when standing up ML experimentation infrastructure or assessing whether a trained model is ready for production.

日本語の概要は準備中です。原文の説明を表示しています。