[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DBGK2YKBJ1QZVGKRVHN692":3,"skill-same:01M6DBGK2YKBJ1QZVGKRVHN692":110},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":33,"linkOnly":34,"markdownContent":35,"markdownBody":36,"frontMatter":37,"refName":38,"commitSha":39,"skillDirectory":40,"forksCount":14,"repositoryHtmlUrl":41,"repositoryHomepageUrl":6,"ownerHtmlUrl":42,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":43,"install":44,"resources":57},"01M6DBGK2YKBJ1QZVGKRVHN692","jupyter-notebook",null,"Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.","Prekzursil\u002Fagent-skills-toolchain","Prekzursil","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F54636077?v=4","01M6DACZ1PCQHD99SCR1YXG28B","Andrei Mihai Visalon","01M6DACZ670WZF535V3WYYSS4Z",0,"MIT","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fjupyter-notebook\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30,31,32],"jupyter notebook","jupyter","notebook","experiments","scaffold","create","generate","run","jupyter notebooks","templates","edit","user","use","clean","2026-11-10 10:12:30",false,"---\nname: \"jupyter-notebook\"\ndescription: \"Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.\"\n---\n\n\n# Jupyter Notebook Skill\n\nCreate clean, reproducible Jupyter notebooks for two primary modes:\n\n- Experiments and exploratory analysis\n- Tutorials and teaching-oriented walkthroughs\n\nPrefer the bundled templates and the helper script for consistent structure and fewer JSON mistakes.\n\n## When to use\n- Create a new `.ipynb` notebook from scratch.\n- Convert rough notes or scripts into a structured notebook.\n- Refactor an existing notebook to be more reproducible and skimmable.\n- Build experiments or tutorials that will be read or re-run by other people.\n\n## Decision tree\n- If the request is exploratory, analytical, or hypothesis-driven, choose `experiment`.\n- If the request is instructional, step-by-step, or audience-specific, choose `tutorial`.\n- If editing an existing notebook, treat it as a refactor: preserve intent and improve structure.\n\n## Skill path (set once)\n\n```bash\nexport CODEX_HOME=\"${CODEX_HOME:-$HOME\u002F.codex}\"\nexport JUPYTER_NOTEBOOK_CLI=\"$CODEX_HOME\u002Fskills\u002Fjupyter-notebook\u002Fscripts\u002Fnew_notebook.py\"\n```\n\nUser-scoped skills install under `$CODEX_HOME\u002Fskills` (default: `~\u002F.codex\u002Fskills`).\n\n## Workflow\n1. Lock the intent.\nIdentify the notebook kind: `experiment` or `tutorial`.\nCapture the objective, audience, and what \"done\" looks like.\n\n2. Scaffold from the template.\nUse the helper script to avoid hand-authoring raw notebook JSON.\n\n```bash\nuv run --python 3.12 python \"$JUPYTER_NOTEBOOK_CLI\" \\\n  --kind experiment \\\n  --title \"Compare prompt variants\" \\\n  --out output\u002Fjupyter-notebook\u002Fcompare-prompt-variants.ipynb\n```\n\n```bash\nuv run --python 3.12 python \"$JUPYTER_NOTEBOOK_CLI\" \\\n  --kind tutorial \\\n  --title \"Intro to embeddings\" \\\n  --out output\u002Fjupyter-notebook\u002Fintro-to-embeddings.ipynb\n```\n\n3. Fill the notebook with small, runnable steps.\nKeep each code cell focused on one step.\nAdd short markdown cells that explain the purpose and expected result.\nAvoid large, noisy outputs when a short summary works.\n\n4. Apply the right pattern.\nFor experiments, follow `references\u002Fexperiment-patterns.md`.\nFor tutorials, follow `references\u002Ftutorial-patterns.md`.\n\n5. Edit safely when working with existing notebooks.\nPreserve the notebook structure; avoid reordering cells unless it improves the top-to-bottom story.\nPrefer targeted edits over full rewrites.\nIf you must edit raw JSON, review `references\u002Fnotebook-structure.md` first.\n\n6. Validate the result.\nRun the notebook top-to-bottom when the environment allows.\nIf execution is not possible, say so explicitly and call out how to validate locally.\nUse the final pass checklist in `references\u002Fquality-checklist.md`.\n\n## Templates and helper script\n- Templates live in `assets\u002Fexperiment-template.ipynb` and `assets\u002Ftutorial-template.ipynb`.\n- The helper script loads a template, updates the title cell, and writes a notebook.\n\nScript path:\n- `$JUPYTER_NOTEBOOK_CLI` (installed default: `$CODEX_HOME\u002Fskills\u002Fjupyter-notebook\u002Fscripts\u002Fnew_notebook.py`)\n\n## Temp and output conventions\n- Use `tmp\u002Fjupyter-notebook\u002F` for intermediate files; delete when done.\n- Write final artifacts under `output\u002Fjupyter-notebook\u002F` when working in this repo.\n- Use stable, descriptive filenames (for example, `ablation-temperature.ipynb`).\n\n## Dependencies (install only when needed)\nPrefer `uv` for dependency management.\n\nOptional Python packages for local notebook execution:\n\n```bash\nuv pip install jupyterlab ipykernel\n```\n\nThe bundled scaffold script uses only the Python standard library and does not require extra dependencies.\n\n## Environment\nNo required environment variables.\n\n## Reference map\n- `references\u002Fexperiment-patterns.md`: experiment structure and heuristics.\n- `references\u002Ftutorial-patterns.md`: tutorial structure and teaching flow.\n- `references\u002Fnotebook-structure.md`: notebook JSON shape and safe editing rules.\n- `references\u002Fquality-checklist.md`: final validation checklist.\n","# Jupyter Notebook Skill\n\nCreate clean, reproducible Jupyter notebooks for two primary modes:\n\n- Experiments and exploratory analysis\n- Tutorials and teaching-oriented walkthroughs\n\nPrefer the bundled templates and the helper script for consistent structure and fewer JSON mistakes.\n\n## When to use\n- Create a new `.ipynb` notebook from scratch.\n- Convert rough notes or scripts into a structured notebook.\n- Refactor an existing notebook to be more reproducible and skimmable.\n- Build experiments or tutorials that will be read or re-run by other people.\n\n## Decision tree\n- If the request is exploratory, analytical, or hypothesis-driven, choose `experiment`.\n- If the request is instructional, step-by-step, or audience-specific, choose `tutorial`.\n- If editing an existing notebook, treat it as a refactor: preserve intent and improve structure.\n\n## Skill path (set once)\n\n```bash\nexport CODEX_HOME=\"${CODEX_HOME:-$HOME\u002F.codex}\"\nexport JUPYTER_NOTEBOOK_CLI=\"$CODEX_HOME\u002Fskills\u002Fjupyter-notebook\u002Fscripts\u002Fnew_notebook.py\"\n```\n\nUser-scoped skills install under `$CODEX_HOME\u002Fskills` (default: `~\u002F.codex\u002Fskills`).\n\n## Workflow\n1. Lock the intent.\nIdentify the notebook kind: `experiment` or `tutorial`.\nCapture the objective, audience, and what \"done\" looks like.\n\n2. Scaffold from the template.\nUse the helper script to avoid hand-authoring raw notebook JSON.\n\n```bash\nuv run --python 3.12 python \"$JUPYTER_NOTEBOOK_CLI\" \\\n  --kind experiment \\\n  --title \"Compare prompt variants\" \\\n  --out output\u002Fjupyter-notebook\u002Fcompare-prompt-variants.ipynb\n```\n\n```bash\nuv run --python 3.12 python \"$JUPYTER_NOTEBOOK_CLI\" \\\n  --kind tutorial \\\n  --title \"Intro to embeddings\" \\\n  --out output\u002Fjupyter-notebook\u002Fintro-to-embeddings.ipynb\n```\n\n3. Fill the notebook with small, runnable steps.\nKeep each code cell focused on one step.\nAdd short markdown cells that explain the purpose and expected result.\nAvoid large, noisy outputs when a short summary works.\n\n4. Apply the right pattern.\nFor experiments, follow `references\u002Fexperiment-patterns.md`.\nFor tutorials, follow `references\u002Ftutorial-patterns.md`.\n\n5. Edit safely when working with existing notebooks.\nPreserve the notebook structure; avoid reordering cells unless it improves the top-to-bottom story.\nPrefer targeted edits over full rewrites.\nIf you must edit raw JSON, review `references\u002Fnotebook-structure.md` first.\n\n6. Validate the result.\nRun the notebook top-to-bottom when the environment allows.\nIf execution is not possible, say so explicitly and call out how to validate locally.\nUse the final pass checklist in `references\u002Fquality-checklist.md`.\n\n## Templates and helper script\n- Templates live in `assets\u002Fexperiment-template.ipynb` and `assets\u002Ftutorial-template.ipynb`.\n- The helper script loads a template, updates the title cell, and writes a notebook.\n\nScript path:\n- `$JUPYTER_NOTEBOOK_CLI` (installed default: `$CODEX_HOME\u002Fskills\u002Fjupyter-notebook\u002Fscripts\u002Fnew_notebook.py`)\n\n## Temp and output conventions\n- Use `tmp\u002Fjupyter-notebook\u002F` for intermediate files; delete when done.\n- Write final artifacts under `output\u002Fjupyter-notebook\u002F` when working in this repo.\n- Use stable, descriptive filenames (for example, `ablation-temperature.ipynb`).\n\n## Dependencies (install only when needed)\nPrefer `uv` for dependency management.\n\nOptional Python packages for local notebook execution:\n\n```bash\nuv pip install jupyterlab ipykernel\n```\n\nThe bundled scaffold script uses only the Python standard library and does not require extra dependencies.\n\n## Environment\nNo required environment variables.\n\n## Reference map\n- `references\u002Fexperiment-patterns.md`: experiment structure and heuristics.\n- `references\u002Ftutorial-patterns.md`: tutorial structure and teaching flow.\n- `references\u002Fnotebook-structure.md`: notebook JSON shape and safe editing rules.\n- `references\u002Fquality-checklist.md`: final validation checklist.\n",{"name":5,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5",".agents\u002Fskills\u002Fjupyter-notebook","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 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genuine pre-execution ambiguity by scanning repo context, generating 1-6 grounded options, and asking 1-3 focused questions via AskUserQuestion. NOT for mid-task use (injection risk); NOT when the goal is already unambiguous; use to disambiguate vague prompts before any file edits.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fworkspace-hooks\u002Fskills\u002Fclarify-requirements\u002FSKILL.md",[],[118,119,120,121,122,123,124,125,126,31,127,128,129,130,131],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","context","repo","injection","execution","file",{"skillNo":133,"name":134,"nameZh":6,"description":135,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":136,"categories":137,"keywords":143,"publishedAt":33},"01M6DF79CA4BHJS66J8EZDBPWJ","openmm-md","Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein \u002F protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fmcp\u002Fopenmm-md-mcp\u002Fskill\u002Fopenmm-md\u002FSKILL.md",[138],{"categoryNo":139,"categoryName":140,"taxonomyType":141,"taxonomyTypeDesc":142},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[144,145,146,147,148,149,150,151,152,153,154,155,156,157,31,158,159,160,161,162],"openmm md","how","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","license","workflow","windows","free","molecular dynamics","local","do","MCP",{"skillNo":164,"name":165,"nameZh":6,"description":166,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":167,"categories":168,"keywords":175,"publishedAt":33},"01M6DF76C1MG85VEWP8VZCBNMN","visual-review","Take screenshots of web pages and UI using Playwright for visual review and iteration","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fvisual-review\u002FSKILL.md",[169,172],{"categoryNo":170,"categoryName":171,"taxonomyType":141,"taxonomyTypeDesc":142},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":173,"categoryName":174,"taxonomyType":141,"taxonomyTypeDesc":142},"01JBSEEDCAT000000000000008","测试与质量",[176,177,178,179,180,181,182,183,184,185,145,186,187,188,189],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":191,"name":192,"nameZh":6,"description":193,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":194,"categories":195,"keywords":196,"publishedAt":33},"01M6DF73AQVCBZKEN0YXEX9FXP","status","Diagnostic status report — shows metaswarm installation state, project setup, and potential issues","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstatus\u002FSKILL.md",[],[192,197,198,199,200,201,202,203],"setup","report","project","installation","project setup","issues","state",{"skillNo":205,"name":206,"nameZh":6,"description":207,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":208,"categories":209,"keywords":211,"publishedAt":33},"01M6DF6X6C2XB0P6GX76P7TTYV","start","Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstart\u002FSKILL.md",[210],{"categoryNo":139,"categoryName":140,"taxonomyType":141,"taxonomyTypeDesc":142},[206,212,123,213,214,215,31,30,216,217,218],"start issue","issue","ready","work on issue","work","work on","development",{"skillNo":220,"name":197,"nameZh":6,"description":221,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":222,"categories":223,"keywords":224,"publishedAt":33},"01M6DF6QMJ9AJKFKHHKRT005PQ","Interactive project setup — detects your project, configures metaswarm, writes project-local files","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fsetup\u002FSKILL.md",[],[197,199,160,225,201,226],"files","interactive"]