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.
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
monetization-strategy
Brainstorm 3-5 monetization strategies with audience fit, risks, and validation experiments. Use when exploring revenue models, evaluating pricing strategies, or deciding how to monetize a product.
mvp
Guide building a minimum viable product the minimalist entrepreneur way — manual first, then processized, then productized. Use when someone is ready to build their first product or struggling with scope.
nature-academic-search
Multi-source literature search, citation verification, MeSH search strategy, citation file management (.nbib/.ris/.bib conversion), and reference management (BibTeX, related articles, ID conversion) via MCP tools (PubMed, CrossRef, arXiv, Scopus, ScienceDirect). Use when the user needs coordinated multi-step literature workflows beyond a single MCP call. Also trigger on general literature-search needs during academic writing even without the word "Nature", such as searching for papers/literature, doing a literature review, verifying a citation, converting citation files, and Chinese phrasings like 文献检索、查文献、找文献、 文献综述检索、查论文、引文核对、参考文献管理、文献去重.
nature-citation
Add strict Nature/CNS citations to manuscript text by splitting long passages into citable segments, searching only accepted flagship and subjournal titles from Nature Portfolio, the AAAS Science family, and Cell Press, filtering by publication time range, and exporting one reference-manager-ready output by default. Use this skill whenever the user asks to input text and automatically get references, add citations to a paragraph/manuscript, find Nature-series or CNS support for statements, create text-to-reference correspondence, "分段引用", "自动给出引用", "Nature系列引用", "CNS及子刊", "支撑文献", "补引用", "找引用", or export EndNote/RIS/ENW/Zotero RDF. Also trigger on general academic-writing citation needs even without the word "Nature", such as adding references while writing a paper, finding sources/literature for a claim, building a reference list, citation/referencing for academic writing, and Chinese phrasings like 学术写作引用、写论文加引用、写paper找文献、加参考文献、配文献、引用文献、文献支撑.
nature-data
Prepare, audit, or revise Nature-ready Data Availability statements, data repository plans, dataset citations, and FAIR metadata checklists for manuscripts. Use when the user asks about Nature data availability, research data sharing, repository selection, accession numbers, restricted or sensitive data, source data, supplementary datasets, DataCite-style dataset references, FAIR metadata for academic publication, or Chinese-to-English data availability wording for Chinese-speaking authors preparing Nature-family submissions. Also trigger on general academic-writing data needs even without the word "Nature", such as writing a data availability statement for any journal, code/data sharing sections, repository selection while writing a paper, and Chinese phrasings like 数据可用性声明、数据可用性、 数据共享、代码可用性、学术写作数据声明、写数据声明、数据存放、数据仓库选择.
nature-figure
Submission-grade Nature/high-impact journal figure workflow for Python or R. Use whenever the user asks to create, revise, audit, or polish manuscript figures, multi-panel scientific plots, figures4papers-style matplotlib plots, or journal-ready SVG/PDF/TIFF outputs, especially for Nature-family or other high-impact journals. Before plotting, define the figure's conclusion, evidence logic, export needs, and review risks. If the user has not chosen Python or R, ask "Python or R?" and stop. Use only the selected backend for figure generation, previewing, exporting, and QA. Supports matplotlib/seaborn and ggplot2/patchwork/ComplexHeatmap. Not for dashboards or Illustrator/Figma-first infographics. Also trigger on general academic-writing figure needs even without the word "Nature", such as making figures/plots for a paper, scientific/academic plotting, data visualization for a manuscript, and Chinese phrasings like 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化.
nature-paper2ppt
Build a complete but efficient Nature-style Chinese PPTX presentation from a scientific paper, preprint, PDF, article text, abstract, figure legends, or reading notes. Use this skill whenever the user asks to make slides/PPT/PPTX for journal club, group meeting, paper sharing, thesis seminar, lab meeting, department report, or academic presentation from a research paper, not only medical papers. It identifies the paper type and argument, selects only the figures needed for the story, writes Chinese slide content and speaker notes, creates the actual .pptx deck, and runs an explicit self-review/corrective revision loop focused on figure quality, text overflow prevention, and non-template visual design before delivery. Also trigger on general academic-presentation requests even without the word "Nature", such as turning a paper into slides, building an academic talk deck, conference/defense presentations, and Chinese phrasings like 论文做PPT、论文汇报、组会PPT、文献汇报、学术汇报、做幻灯片、讲paper、读书报告PPT.
nature-polishing
Polish, restructure, or translate academic prose into Nature-leaning English using writing-strategy principles, curated Nature/Nature Communications article patterns, and phrase-level support from Academic Phrasebank. Use whenever the user asks to polish a manuscript paragraph, abstract, introduction, results, discussion, conclusion, title, methods section, or Chinese academic draft for publication-quality English. Also covers LaTeX layout/typesetting (排版) fixes — loose or sparse pages, stranded section headings, figures that don't fill the page or split across pages, "Float too large", multi-panel figure arrangement, and Supplementary Information that looks empty — via references/latex-layout.md. Also trigger on general academic/scientific writing requests even without the word "Nature", including academic writing, scientific writing, SCI/paper writing, English manuscript polishing, language editing, proofreading, and Chinese phrasings such as 学术写作、科研写作、论文润色、写paper、SCI写作、英文论文润色、语言润色、润色、改写、学术英语、英文写作.
nature-reader
Build full-paper Chinese-English side-by-side, figure/table-aware, source-grounded Markdown readers for journal or conference papers from PDF, DOI, arXiv, publisher HTML, or pasted text. Use whenever the user asks to translate or read a paper, make 中英文对照/原文对照/全文翻译解读, extract figures or tables into the right positions, preserve figure/table placement near relevant prose, or keep exact source anchors for every block. This skill must not degrade into a summary-only output unless the user explicitly asks for a summary. Also trigger on general paper-reading and translation requests even without the word "Nature", such as reading/translating an academic paper, literature reading, understanding a paper, and Chinese phrasings like 读论文、精读论文、论文翻译、文献翻译、文献阅读、学术阅读、帮我读这篇文章、翻译这篇paper.
nature-response
Draft, audit, or revise point-by-point reviewer response letters for Nature-family manuscript revisions. Use when the user provides reviewer comments, editor decision letters, revision notes, response drafts, or asks how to respond to major/minor revision requests, rebuttal letters, response to reviewers, peer-review reports, 审稿意见回复, 逐点回复, 修回信, 大修回复, 小修回复, or 如何回复 reviewer. Also trigger on general peer-review response needs during academic writing/revision even without the word "Nature", such as replying to reviewers for any journal, writing a rebuttal/response letter, handling revision comments, and Chinese phrasings like 回复审稿人、审稿回复、返修、 修改稿回复、写rebuttal、回应审稿意见、应对审稿.
nature-reviewer
Simulate a Nature-style reviewer assessment from the referee perspective rather than an author rebuttal. Use when the user wants a pre-submission review, reviewer report, peer-review style critique, novelty/significance/technical soundness assessment, reviewer-style manuscript evaluation, 审稿人视角评估, 预审稿意见, or Nature reviewer report. Return 3 reviewer reports plus a cross-review synthesis, grounded only in the local Nature reviewer source basis. Also trigger on general pre-submission review requests during academic writing even without the word "Nature", such as getting a mock peer review for any journal, critiquing a draft as a reviewer would, assessing novelty/rigor before submission, and Chinese phrasings like 审稿人视角、模拟审稿、预审、帮我审一下论文、投稿前自审、审稿意见模拟、找论文问题.
nature-writing
Draft, restructure, or plan Nature-style manuscript sections from author-provided claims, results, figures, notes, or Chinese drafts. Use when the user wants to write or rebuild an abstract, introduction, related-work, method, experiments, discussion, conclusion, title, or full manuscript argument rather than only polish finished prose. Also trigger on general academic-writing requests even without the word "Nature", such as writing a paper from scratch, drafting a manuscript/section, structuring a paper, and Chinese phrasings like 学术写作、科研写作、论文写作、写论文、写paper、SCI写作、帮我写论文、搭论文框架、起草论文、写引言/摘要/讨论.
networkx
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
neurokit2
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
neuropixels-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.
nextflow
Build, run, and debug Nextflow data pipelines and nf-core workflows end to end. Use whenever the user mentions Nextflow, nf-core, .nf files, nextflow.config, DSL2, processes/channels/operators, samplesheets, or wants to run a community pipeline (e.g. nf-core/rnaseq, nf-core/sarek), write or test a module/subworkflow with nf-test, configure executors/containers (Docker, Singularity/Apptainer, Conda, Wave), scale a workflow to HPC/SLURM or cloud (AWS Batch, Google Batch, Azure, Kubernetes), or debug a failed/-resume run. Make sure to use this skill for any reproducible scientific/bioinformatics workflow work even if the user does not say the word "Nextflow", and for authoring nf-core-compliant pipelines, modules, configs, and linting.
north-star-metric
Define a North Star Metric and 3-5 supporting input metrics that form a metrics constellation. Classify the business game (Attention, Transaction, Productivity) and validate against 7 criteria for an effective North Star. Use when choosing a North Star Metric, setting up a metrics framework, learning about the North Star Framework, or deciding what to measure.
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.