生物化学家与生物物理学家

Literature Review

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

Molecular Dynamics

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

Pyopenms

Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

Matchms

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

生物信息学

Neuropixels Data Analysis

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

Glycoengineering

Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.

Scientific Writing

Academic manuscript writing with IMRAD structure, citation formatting, and reporting guidelines. Use when drafting or revising research papers.

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数据分析

Hypothesis Formulation

Structured scientific hypothesis generation from observations. Use when formulating testable hypotheses, competing explanations, or experimental predictions.

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Literature Search

Systematic literature review methodology including search strategy, screening, and synthesis. Use when conducting literature reviews or writing background sections.

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实验室工具

Result To Claim

Use when experiments complete to judge what claims the results support, what they do not, and what evidence is still missing. A secondary Codex agent evaluates results against intended claims and routes to the next action (pivot, supplement, or confirm). Use after experiments finish - before writing the paper or running ablations.

Deepxiv

Search and progressively read open-access academic papers through DeepXiv. Use when the user wants layered paper access, section-level reading, trending papers, or DeepXiv-backed literature retrieval.

Ablation Planner

Use when main results pass result-to-claim (`claim_supported = yes` or `partial`) and ablation studies are needed for paper submission. A secondary Codex agent designs ablations from a reviewer's perspective; the local executor reviews feasibility and implements.

Deepxiv

Search and progressively read open-access academic papers through DeepXiv. Use when the user wants layered paper access, section-level reading, trending papers, or DeepXiv-backed literature retrieval.

CI/CD

Rebuttal

Workflow 4: Submission rebuttal pipeline. Parses external reviews, enforces coverage and grounding, drafts a safe text-only rebuttal under venue limits, and manages follow-up rounds.

生物信息学

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.

3d Molecule Ray Tracer

Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.

金融与投资

Grant Thinking Cn Biology

Use when evaluating biology grant ideas in the Chinese funding context (NSFC, MOST, etc.) — diagnosing project legitimacy, mechanism-centered scientific questions, reviewer-aware logic, innovation discipline, feasibility, and scope control across funding levels (youth, general, key).

效率与集成

Literature Daily Report

每日科研文献日报生成与管理。当用户请求生成科研日报、更新文献收集脚本或分析研究趋势时激活。支持：(1) 自动抓取 PubMed/bioRxiv/arXiv 最新文献，(2) 语义筛选 AI/生信/病原/真菌等领域，(3) LLM 智能总结与编辑排版，(4) 中文格式报告输出，(5) Zotero 自动录入，(6) 知识图谱同步。

Scientific Thinking

Use when interpreting research findings, evaluating scientific evidence, analyzing mechanisms, comparing competing hypotheses, designing experiments, or constructing scientific arguments.

Reagent Substitute Scout

Find validated alternative reagents based on literature citation data.

效率与集成

Literature Daily Report

每日科研文献日报生成与管理。当用户请求生成科研日报、更新文献收集脚本或分析研究趋势时激活。支持：(1) 自动抓取 PubMed/bioRxiv/arXiv 最新文献，(2) 语义筛选 AI/生信/病原/真菌等领域，(3) LLM 智能总结与编辑排版，(4) 中文格式报告输出与定时任务管理。

Research Automation

Automated web research for peptides, biohacking protocols, longevity science, and trending health topics. Use when you need to discover new information, track emerging trends, monitor scientific updates, or generate content ideas based on current research. Runs periodically via heartbeat or on-demand.

实验室工具

Smart Journal Monitor

Use smart journal monitor for evidence insight workflows that need structured execution, explicit assumptions, and clear output boundaries.

Automd Gromacs

AutoMD-GROMACS: Automated molecular dynamics simulation workflow - 13 Skills covering system setup, equilibration, production, analysis, free energy, ligand binding, membrane proteins, umbrella sampling, PCA, and workflows. Built-in auto-repair, 84.7% token savings. Part of the AutoMD series.

实验室工具

Experiment Notes

Track, search, and learn from experiments. Automatic logging of trial-and-error, success/failure patterns, and distilled lessons. Prevents repeating mistakes.

Biorxiv

Access bioRxiv preprint repository for biology preprints. Use for: (1) Fetching recent preprints from specific categories like bioinformatics, genomics, molecular-biology, etc., (2) Getting papers by date range, (3) Listing available subject collections, (4) Retrieving paper metadata including titles, authors, DOIs, dates, and categories. No authentication required.

调试

GO/KEGG Enrichment Analysis

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)

监控

Primer Design Check

Check primers for dimers, hairpins, and off-target amplification