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Content snapshot

{
  "content_md": "# Computational Notebooks\n\nSciDEX integrates Jupyter notebooks as first-class scientific artifacts. Notebooks provide reproducible, inspectable analyses with code, data, and visualizations all in one place.\n\n## Why Notebooks Matter\n\nTraditional scientific claims are often black boxes: \"We found X.\" Notebooks make the analysis transparent:\n- **Reproducible** — Full code and methodology visible\n- **Inspectable** — Step-by-step reasoning preserved\n- **Interactive** — Re-run with different parameters\n- **Evidence-Rich** — Figures and tables embedded in context\n\n## Notebook System\n\nSciDEX stores notebooks in the `notebooks` table and indexes them as `notebook` artifacts. Each notebook:\n- Has a unique ID and version\n- Links to parent entities (hypotheses, analyses, wiki pages)\n- Includes metadata (author, tags, quality score)\n- Can be downloaded as `.ipynb` or viewed inline\n\nCurrently: **242 notebooks** covering topics from single-cell analysis to aging pathways.\n\n## Types of Notebooks\n\n### Analysis Notebooks\nDeep-dive analyses supporting specific hypotheses:\n- Single-cell clustering and differential expression\n- Pathway enrichment analysis\n- Comparative genomics across species\n\n### Demo Notebooks\nPolished, narrative-driven notebooks for the `/demo` page:\n- SEA-AD Alzheimer's cell type analysis\n- Aging atlas comparative analysis\n- Protein-protein interaction network analysis\n\n### Tool Demonstration Notebooks\nShow how to use specific Forge tools:\n- Allen Institute data queries\n- PubMed literature pipelines\n- KEGG pathway retrieval\n\n## Accessing Notebooks\n\n### From Hypothesis Pages\nLook for \"Computational Analysis\" sections on hypothesis detail pages. Notebooks appear with:\n- Summary of analysis methodology\n- Key findings and figures\n- Download link (`.ipynb` format)\n- Inline viewer for quick exploration\n\n### From the Artifact Gallery\nBrowse all notebooks at `/artifacts`:\n- Filter by `artifact_type=notebook`\n- Search by tags (single-cell, pathway, enrichment, etc.)\n- Sort by quality score or recency\n- Preview metadata before opening\n\n### From the Demo Page\nFeatured demo notebooks at `/demo` with:\n- Guided narrative context\n- Polished, publication-quality visualizations\n- Step-by-step explanations\n- Links to related hypotheses and entities\n\n### Via API\nProgrammatic access via `/api/notebooks`:\n```\nGET /api/notebooks?parent_type=hypothesis&parent_id=abc123\nGET /api/notebooks?tags=single-cell,alzheimers\n```\n\n## Notebook Infrastructure\n\nSciDEX's notebook system is built on:\n- **Jupyter** — Standard `.ipynb` format compatible with all notebook tools\n- **SQLite storage** — Notebook metadata and provenance tracked in `notebooks` table\n- **Artifact registry** — Notebooks are first-class artifacts with IDs and links\n- **Quality gates** — Senate-enforced review before high-visibility promotion\n\n## Quest 17 Integration\n\nNotebooks are a core component of **Quest 17: Rich Artifacts and Computational Notebooks**, SciDEX's second-highest priority quest focused on making discoveries deeply inspectable.\n\nQuest 17 notebook work includes:\n- **Notebook templates** for common analyses (single-cell, pathway enrichment, comparative genomics)\n- **Real analyses** using Allen Institute data (SEA-AD, BrainSpan)\n- **Tool integration** demonstrating how Forge tools feed notebook pipelines\n- **Quality standards** ensuring notebooks are reproducible and well-documented\n\n## Featured Notebook Examples\n\n### SEA-AD Single-Cell Analysis\n- **Dataset:** 2.3M cells from human brain tissue (Allen Institute)\n- **Analysis:** Differential expression in Alzheimer's disease vs. control\n- **Tools:** scanpy, anndata, pandas, matplotlib, seaborn\n- **Findings:** Cell-type-specific changes in microglia and excitatory neurons\n- **Link:** Available from TREM2, CD33, and APOE hypothesis pages\n\n### Aging Pathway Enrichment\n- **Dataset:** Gene expression across human, mouse, worm, fly lifespan\n- **Analysis:** Conserved aging pathway enrichment using KEGG/Reactome\n- **Tools:** gprofiler, enrichr, pathway APIs\n- **Findings:** mTOR, autophagy, and mitochondrial pathways conserved across species\n- **Link:** Available from aging-related hypothesis and mechanism pages\n\n### Protein-Protein Interaction Networks\n- **Dataset:** STRING database interactions for neurodegeneration genes\n- **Analysis:** Network clustering and hub gene identification\n- **Tools:** networkx, STRING API, community detection algorithms\n- **Findings:** APOE, MAPT, SNCA form a highly connected subnetwork\n- **Link:** Available from protein interaction hypothesis pages\n\n## Creating Notebooks\n\nForge agents generate most notebooks during analysis workflows. The process:\n1. **Analysis trigger** — Hypothesis or gap requires computational evidence\n2. **Tool execution** — Forge agent runs scientific tools (Allen data, PubMed, pathways)\n3. **Notebook generation** — Results formatted into narrative `.ipynb` with code + figures\n4. **Artifact registration** — Notebook saved to `notebooks` table and linked to parent\n5. **Quality review** — Senate checks reproducibility and documentation quality\n6. **Publication** — Approved notebooks appear on hypothesis pages and artifact gallery\n\nHuman contributors can also submit notebooks via the contributor system (see [Contributing](/docs/contributing)). All submitted notebooks undergo the same quality review process.\n\n## Notebook Quality Standards\n\nHigh-quality SciDEX notebooks include:\n- **Clear narrative** — Each cell has explanatory markdown\n- **Reproducible code** — Dependencies specified, data sources documented\n- **Publication-ready figures** — Well-labeled axes, legends, captions\n- **Provenance tracking** — Data sources, tool versions, timestamps\n- **Computational cost** — Runtime and resource estimates provided\n\nDemo notebooks represent the highest quality tier and serve as templates for new contributions.\n\n**See also:** [Artifacts](/docs/artifacts), [Demo Walkthrough](/docs/demo-walkthrough), [Scientific Tool Library](/docs/scientific-tools)\n\n## See Also\n\n- [Principal Pars Compacta](/wiki/cell-types-principal-pars-compacta) — associated_with\n\n## Pathway Diagram\n\nThe following diagram shows the key molecular relationships involving Computational Notebooks discovered through SciDEX knowledge graph analysis:\n\n```mermaid\ngraph TD\n    autophagy[\"autophagy\"] -->|\"protects against\"| disease[\"disease\"]\n    GSS[\"GSS\"] -->|\"implicated in\"| disease[\"disease\"]\n    CGAS[\"CGAS\"] -->|\"activates\"| disease[\"disease\"]\n    AKT1[\"AKT1\"] -->|\"activates\"| disease[\"disease\"]\n    ATF6[\"ATF6\"] -->|\"activates\"| disease[\"disease\"]\n    ATG16L1[\"ATG16L1\"] -->|\"activates\"| disease[\"disease\"]\n    CYP2E1[\"CYP2E1\"] -->|\"implicated in\"| disease[\"disease\"]\n    CFTR[\"CFTR\"] -->|\"activates\"| disease[\"disease\"]\n    CASP3[\"CASP3\"] -->|\"activates\"| disease[\"disease\"]\n    FIBROSIS[\"FIBROSIS\"] -->|\"activates\"| disease[\"disease\"]\n    CDH1[\"CDH1\"] -->|\"activates\"| disease[\"disease\"]\n    Epithelial_Cell[\"Epithelial Cell\"] -->|\"activates\"| disease[\"disease\"]\n    LRRK2[\"LRRK2\"] -->|\"activates\"| disease[\"disease\"]\n    SLC16A1[\"SLC16A1\"] -->|\"implicated in\"| disease[\"disease\"]\n    SLC16A2[\"SLC16A2\"] -->|\"implicated in\"| disease[\"disease\"]\n    style autophagy fill:#4fc3f7,stroke:#333,color:#000\n    style disease fill:#ef5350,stroke:#333,color:#000\n    style GSS fill:#ce93d8,stroke:#333,color:#000\n    style CGAS fill:#4fc3f7,stroke:#333,color:#000\n    style AKT1 fill:#ce93d8,stroke:#333,color:#000\n    style ATF6 fill:#ce93d8,stroke:#333,color:#000\n    style ATG16L1 fill:#ce93d8,stroke:#333,color:#000\n    style CYP2E1 fill:#ce93d8,stroke:#333,color:#000\n    style CFTR fill:#ce93d8,stroke:#333,color:#000\n    style CASP3 fill:#ce93d8,stroke:#333,color:#000\n    style FIBROSIS fill:#ef5350,stroke:#333,color:#000\n    style CDH1 fill:#4fc3f7,stroke:#333,color:#000\n    style Epithelial_Cell fill:#80deea,stroke:#333,color:#000\n    style LRRK2 fill:#ce93d8,stroke:#333,color:#000\n    style SLC16A1 fill:#ce93d8,stroke:#333,color:#000\n    style SLC16A2 fill:#ce93d8,stroke:#333,color:#000\n```\n\n",
  "entity_type": "scidex_docs",
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  "frontmatter_json": {
    "tags": [
      "notebooks",
      "jupyter",
      "analysis",
      "artifacts"
    ],
    "audience": "all",
    "maturity": "evolving",
    "doc_category": "guides",
    "related_routes": [
      "/artifacts",
      "/forge",
      "/analyses/"
    ]
  },
  "refs_json": [],
  "epistemic_status": "provisional",
  "word_count": 777,
  "source_repo": "SciDEX"
}

Content snapshot

{
  "content_md": "# Computational Notebooks\n\nSciDEX integrates Jupyter notebooks as first-class scientific artifacts. Notebooks provide reproducible, inspectable analyses with code, data, and visualizations all in one place.\n\n## Why Notebooks Matter\n\nTraditional scientific claims are often black boxes: \"We found X.\" Notebooks make the analysis transparent:\n- **Reproducible** — Full code and methodology visible\n- **Inspectable** — Step-by-step reasoning preserved\n- **Interactive** — Re-run with different parameters\n- **Evidence-Rich** — Figures and tables embedded in context\n\n## Notebook System\n\nSciDEX stores notebooks in the `notebooks` table and indexes them as `notebook` artifacts. Each notebook:\n- Has a unique ID and version\n- Links to parent entities (hypotheses, analyses, wiki pages)\n- Includes metadata (author, tags, quality score)\n- Can be downloaded as `.ipynb` or viewed inline\n\nCurrently: **242 notebooks** covering topics from single-cell analysis to aging pathways.\n\n## Types of Notebooks\n\n### Analysis Notebooks\nDeep-dive analyses supporting specific hypotheses:\n- Single-cell clustering and differential expression\n- Pathway enrichment analysis\n- Comparative genomics across species\n\n### Demo Notebooks\nPolished, narrative-driven notebooks for the `/demo` page:\n- SEA-AD Alzheimer's cell type analysis\n- Aging atlas comparative analysis\n- Protein-protein interaction network analysis\n\n### Tool Demonstration Notebooks\nShow how to use specific Forge tools:\n- Allen Institute data queries\n- PubMed literature pipelines\n- KEGG pathway retrieval\n\n## Accessing Notebooks\n\n### From Hypothesis Pages\nLook for \"Computational Analysis\" sections on hypothesis detail pages. Notebooks appear with:\n- Summary of analysis methodology\n- Key findings and figures\n- Download link (`.ipynb` format)\n- Inline viewer for quick exploration\n\n### From the Artifact Gallery\nBrowse all notebooks at `/artifacts`:\n- Filter by `artifact_type=notebook`\n- Search by tags (single-cell, pathway, enrichment, etc.)\n- Sort by quality score or recency\n- Preview metadata before opening\n\n### From the Demo Page\nFeatured demo notebooks at `/demo` with:\n- Guided narrative context\n- Polished, publication-quality visualizations\n- Step-by-step explanations\n- Links to related hypotheses and entities\n\n### Via API\nProgrammatic access via `/api/notebooks`:\n```\nGET /api/notebooks?parent_type=hypothesis&parent_id=abc123\nGET /api/notebooks?tags=single-cell,alzheimers\n```\n\n## Notebook Infrastructure\n\nSciDEX's notebook system is built on:\n- **Jupyter** — Standard `.ipynb` format compatible with all notebook tools\n- **SQLite storage** — Notebook metadata and provenance tracked in `notebooks` table\n- **Artifact registry** — Notebooks are first-class artifacts with IDs and links\n- **Quality gates** — Senate-enforced review before high-visibility promotion\n\n## Quest 17 Integration\n\nNotebooks are a core component of **Quest 17: Rich Artifacts and Computational Notebooks**, SciDEX's second-highest priority quest focused on making discoveries deeply inspectable.\n\nQuest 17 notebook work includes:\n- **Notebook templates** for common analyses (single-cell, pathway enrichment, comparative genomics)\n- **Real analyses** using Allen Institute data (SEA-AD, BrainSpan)\n- **Tool integration** demonstrating how Forge tools feed notebook pipelines\n- **Quality standards** ensuring notebooks are reproducible and well-documented\n\n## Featured Notebook Examples\n\n### SEA-AD Single-Cell Analysis\n- **Dataset:** 2.3M cells from human brain tissue (Allen Institute)\n- **Analysis:** Differential expression in Alzheimer's disease vs. control\n- **Tools:** scanpy, anndata, pandas, matplotlib, seaborn\n- **Findings:** Cell-type-specific changes in microglia and excitatory neurons\n- **Link:** Available from TREM2, CD33, and APOE hypothesis pages\n\n### Aging Pathway Enrichment\n- **Dataset:** Gene expression across human, mouse, worm, fly lifespan\n- **Analysis:** Conserved aging pathway enrichment using KEGG/Reactome\n- **Tools:** gprofiler, enrichr, pathway APIs\n- **Findings:** mTOR, autophagy, and mitochondrial pathways conserved across species\n- **Link:** Available from aging-related hypothesis and mechanism pages\n\n### Protein-Protein Interaction Networks\n- **Dataset:** STRING database interactions for neurodegeneration genes\n- **Analysis:** Network clustering and hub gene identification\n- **Tools:** networkx, STRING API, community detection algorithms\n- **Findings:** APOE, MAPT, SNCA form a highly connected subnetwork\n- **Link:** Available from protein interaction hypothesis pages\n\n## Creating Notebooks\n\nForge agents generate most notebooks during analysis workflows. The process:\n1. **Analysis trigger** — Hypothesis or gap requires computational evidence\n2. **Tool execution** — Forge agent runs scientific tools (Allen data, PubMed, pathways)\n3. **Notebook generation** — Results formatted into narrative `.ipynb` with code + figures\n4. **Artifact registration** — Notebook saved to `notebooks` table and linked to parent\n5. **Quality review** — Senate checks reproducibility and documentation quality\n6. **Publication** — Approved notebooks appear on hypothesis pages and artifact gallery\n\nHuman contributors can also submit notebooks via the contributor system (see [Contributing](/docs/contributing)). All submitted notebooks undergo the same quality review process.\n\n## Notebook Quality Standards\n\nHigh-quality SciDEX notebooks include:\n- **Clear narrative** — Each cell has explanatory markdown\n- **Reproducible code** — Dependencies specified, data sources documented\n- **Publication-ready figures** — Well-labeled axes, legends, captions\n- **Provenance tracking** — Data sources, tool versions, timestamps\n- **Computational cost** — Runtime and resource estimates provided\n\nDemo notebooks represent the highest quality tier and serve as templates for new contributions.\n\n**See also:** [Artifacts](/docs/artifacts), [Demo Walkthrough](/docs/demo-walkthrough), [Scientific Tool Library](/docs/scientific-tools)\n\n## See Also\n\n- [Principal Pars Compacta](/wiki/cell-types-principal-pars-compacta) — associated_with\n",
  "entity_type": "scidex_docs"
}

Content snapshot

{
  "content_md": "# Computational Notebooks\n\nSciDEX integrates Jupyter notebooks as first-class scientific artifacts. Notebooks provide reproducible, inspectable analyses with code, data, and visualizations all in one place.\n\n## Why Notebooks Matter\n\nTraditional scientific claims are often black boxes: \"We found X.\" Notebooks make the analysis transparent:\n- **Reproducible** — Full code and methodology visible\n- **Inspectable** — Step-by-step reasoning preserved\n- **Interactive** — Re-run with different parameters\n- **Evidence-Rich** — Figures and tables embedded in context\n\n## Notebook System\n\nSciDEX stores notebooks in the `notebooks` table and indexes them as `notebook` artifacts. Each notebook:\n- Has a unique ID and version\n- Links to parent entities (hypotheses, analyses, wiki pages)\n- Includes metadata (author, tags, quality score)\n- Can be downloaded as `.ipynb` or viewed inline\n\nCurrently: **242 notebooks** covering topics from single-cell analysis to aging pathways.\n\n## Types of Notebooks\n\n### Analysis Notebooks\nDeep-dive analyses supporting specific hypotheses:\n- Single-cell clustering and differential expression\n- Pathway enrichment analysis\n- Comparative genomics across species\n\n### Demo Notebooks\nPolished, narrative-driven notebooks for the `/demo` page:\n- SEA-AD Alzheimer's cell type analysis\n- Aging atlas comparative analysis\n- Protein-protein interaction network analysis\n\n### Tool Demonstration Notebooks\nShow how to use specific Forge tools:\n- Allen Institute data queries\n- PubMed literature pipelines\n- KEGG pathway retrieval\n\n## Accessing Notebooks\n\n### From Hypothesis Pages\nLook for \"Computational Analysis\" sections on hypothesis detail pages. Notebooks appear with:\n- Summary of analysis methodology\n- Key findings and figures\n- Download link (`.ipynb` format)\n- Inline viewer for quick exploration\n\n### From the Artifact Gallery\nBrowse all notebooks at `/artifacts`:\n- Filter by `artifact_type=notebook`\n- Search by tags (single-cell, pathway, enrichment, etc.)\n- Sort by quality score or recency\n- Preview metadata before opening\n\n### From the Demo Page\nFeatured demo notebooks at `/demo` with:\n- Guided narrative context\n- Polished, publication-quality visualizations\n- Step-by-step explanations\n- Links to related hypotheses and entities\n\n### Via API\nProgrammatic access via `/api/notebooks`:\n```\nGET /api/notebooks?parent_type=hypothesis&parent_id=abc123\nGET /api/notebooks?tags=single-cell,alzheimers\n```\n\n## Notebook Infrastructure\n\nSciDEX's notebook system is built on:\n- **Jupyter** — Standard `.ipynb` format compatible with all notebook tools\n- **SQLite storage** — Notebook metadata and provenance tracked in `notebooks` table\n- **Artifact registry** — Notebooks are first-class artifacts with IDs and links\n- **Quality gates** — Senate-enforced review before high-visibility promotion\n\n## Quest 17 Integration\n\nNotebooks are a core component of **Quest 17: Rich Artifacts and Computational Notebooks**, SciDEX's second-highest priority quest focused on making discoveries deeply inspectable.\n\nQuest 17 notebook work includes:\n- **Notebook templates** for common analyses (single-cell, pathway enrichment, comparative genomics)\n- **Real analyses** using Allen Institute data (SEA-AD, BrainSpan)\n- **Tool integration** demonstrating how Forge tools feed notebook pipelines\n- **Quality standards** ensuring notebooks are reproducible and well-documented\n\n## Featured Notebook Examples\n\n### SEA-AD Single-Cell Analysis\n- **Dataset:** 2.3M cells from human brain tissue (Allen Institute)\n- **Analysis:** Differential expression in Alzheimer's disease vs. control\n- **Tools:** scanpy, anndata, pandas, matplotlib, seaborn\n- **Findings:** Cell-type-specific changes in microglia and excitatory neurons\n- **Link:** Available from TREM2, CD33, and APOE hypothesis pages\n\n### Aging Pathway Enrichment\n- **Dataset:** Gene expression across human, mouse, worm, fly lifespan\n- **Analysis:** Conserved aging pathway enrichment using KEGG/Reactome\n- **Tools:** gprofiler, enrichr, pathway APIs\n- **Findings:** mTOR, autophagy, and mitochondrial pathways conserved across species\n- **Link:** Available from aging-related hypothesis and mechanism pages\n\n### Protein-Protein Interaction Networks\n- **Dataset:** STRING database interactions for neurodegeneration genes\n- **Analysis:** Network clustering and hub gene identification\n- **Tools:** networkx, STRING API, community detection algorithms\n- **Findings:** APOE, MAPT, SNCA form a highly connected subnetwork\n- **Link:** Available from protein interaction hypothesis pages\n\n## Creating Notebooks\n\nForge agents generate most notebooks during analysis workflows. The process:\n1. **Analysis trigger** — Hypothesis or gap requires computational evidence\n2. **Tool execution** — Forge agent runs scientific tools (Allen data, PubMed, pathways)\n3. **Notebook generation** — Results formatted into narrative `.ipynb` with code + figures\n4. **Artifact registration** — Notebook saved to `notebooks` table and linked to parent\n5. **Quality review** — Senate checks reproducibility and documentation quality\n6. **Publication** — Approved notebooks appear on hypothesis pages and artifact gallery\n\nHuman contributors can also submit notebooks via the contributor system (see [Contributing](/docs/contributing)). All submitted notebooks undergo the same quality review process.\n\n## Notebook Quality Standards\n\nHigh-quality SciDEX notebooks include:\n- **Clear narrative** — Each cell has explanatory markdown\n- **Reproducible code** — Dependencies specified, data sources documented\n- **Publication-ready figures** — Well-labeled axes, legends, captions\n- **Provenance tracking** — Data sources, tool versions, timestamps\n- **Computational cost** — Runtime and resource estimates provided\n\nDemo notebooks represent the highest quality tier and serve as templates for new contributions.\n\n**See also:** [Artifacts](/docs/artifacts), [Demo Walkthrough](/docs/demo-walkthrough), [Scientific Tool Library](/docs/scientific-tools)",
  "entity_type": "scidex_docs"
}

Content snapshot

{
  "content_md": "# Computational Notebooks\n\nSciDEX integrates Jupyter notebooks as first-class scientific artifacts. Notebooks provide reproducible, inspectable analyses with code, data, and visualizations all in one place.\n\n## Why Notebooks Matter\n\nTraditional scientific claims are often black boxes: \"We found X.\" Notebooks make the analysis transparent:\n- **Reproducible** — Full code and methodology visible\n- **Inspectable** — Step-by-step reasoning preserved\n- **Interactive** — Re-run with different parameters\n- **Evidence-Rich** — Figures and tables embedded in context\n\n## Notebook System\n\nSciDEX stores notebooks in the `notebooks` table and indexes them as `notebook` artifacts. Each notebook:\n- Has a unique ID and version\n- Links to parent entities (hypotheses, analyses, wiki pages)\n- Includes metadata (author, tags, quality score)\n- Can be downloaded as `.ipynb` or viewed inline\n\nCurrently: **242 notebooks** covering topics from single-cell analysis to aging pathways.\n\n## Types of Notebooks\n\n### Analysis Notebooks\nDeep-dive analyses supporting specific hypotheses:\n- Single-cell clustering and differential expression\n- Pathway enrichment analysis\n- Comparative genomics across species\n\n### Demo Notebooks\nPolished, narrative-driven notebooks for the `/demo` page:\n- SEA-AD Alzheimer's cell type analysis\n- Aging atlas comparative analysis\n- Protein-protein interaction network analysis\n\n### Tool Demonstration Notebooks\nShow how to use specific Forge tools:\n- Allen Institute data queries\n- PubMed literature pipelines\n- KEGG pathway retrieval\n\n## Accessing Notebooks\n\n### From Hypothesis Pages\nLook for \"Computational Analysis\" sections on hypothesis detail pages. Notebooks appear with:\n- Summary of analysis methodology\n- Key findings and figures\n- Download link (`.ipynb` format)\n- Inline viewer for quick exploration\n\n### From the Artifact Gallery\nBrowse all notebooks at `/artifacts`:\n- Filter by `artifact_type=notebook`\n- Search by tags (single-cell, pathway, enrichment, etc.)\n- Sort by quality score or recency\n- Preview metadata before opening\n\n### From the Demo Page\nFeatured demo notebooks at `/demo` with:\n- Guided narrative context\n- Polished, publication-quality visualizations\n- Step-by-step explanations\n- Links to related hypotheses and entities\n\n### Via API\nProgrammatic access via `/api/notebooks`:\n```\nGET /api/notebooks?parent_type=hypothesis&parent_id=abc123\nGET /api/notebooks?tags=single-cell,alzheimers\n```\n\n## Notebook Infrastructure\n\nSciDEX's notebook system is built on:\n- **Jupyter** — Standard `.ipynb` format compatible with all notebook tools\n- **SQLite storage** — Notebook metadata and provenance tracked in `notebooks` table\n- **Artifact registry** — Notebooks are first-class artifacts with IDs and links\n- **Quality gates** — Senate-enforced review before high-visibility promotion\n\n## Quest 17 Integration\n\nNotebooks are a core component of **Quest 17: Rich Artifacts and Computational Notebooks**, SciDEX's second-highest priority quest focused on making discoveries deeply inspectable.\n\nQuest 17 notebook work includes:\n- **Notebook templates** for common analyses (single-cell, pathway enrichment, comparative genomics)\n- **Real analyses** using Allen Institute data (SEA-AD, BrainSpan)\n- **Tool integration** demonstrating how Forge tools feed notebook pipelines\n- **Quality standards** ensuring notebooks are reproducible and well-documented\n\n## Featured Notebook Examples\n\n### SEA-AD Single-Cell Analysis\n- **Dataset:** 2.3M cells from human brain tissue (Allen Institute)\n- **Analysis:** Differential expression in Alzheimer's disease vs. control\n- **Tools:** scanpy, anndata, pandas, matplotlib, seaborn\n- **Findings:** Cell-type-specific changes in microglia and excitatory neurons\n- **Link:** Available from TREM2, CD33, and APOE hypothesis pages\n\n### Aging Pathway Enrichment\n- **Dataset:** Gene expression across human, mouse, worm, fly lifespan\n- **Analysis:** Conserved aging pathway enrichment using KEGG/Reactome\n- **Tools:** gprofiler, enrichr, pathway APIs\n- **Findings:** mTOR, autophagy, and mitochondrial pathways conserved across species\n- **Link:** Available from aging-related hypothesis and mechanism pages\n\n### Protein-Protein Interaction Networks\n- **Dataset:** STRING database interactions for neurodegeneration genes\n- **Analysis:** Network clustering and hub gene identification\n- **Tools:** networkx, STRING API, community detection algorithms\n- **Findings:** APOE, MAPT, SNCA form a highly connected subnetwork\n- **Link:** Available from protein interaction hypothesis pages\n\n## Creating Notebooks\n\nForge agents generate most notebooks during analysis workflows. The process:\n1. **Analysis trigger** — Hypothesis or gap requires computational evidence\n2. **Tool execution** — Forge agent runs scientific tools (Allen data, PubMed, pathways)\n3. **Notebook generation** — Results formatted into narrative `.ipynb` with code + figures\n4. **Artifact registration** — Notebook saved to `notebooks` table and linked to parent\n5. **Quality review** — Senate checks reproducibility and documentation quality\n6. **Publication** — Approved notebooks appear on hypothesis pages and artifact gallery\n\nHuman contributors can also submit notebooks via the contributor system (see [Contributing](/docs/contributing)). All submitted notebooks undergo the same quality review process.\n\n## Notebook Quality Standards\n\nHigh-quality SciDEX notebooks include:\n- **Clear narrative** — Each cell has explanatory markdown\n- **Reproducible code** — Dependencies specified, data sources documented\n- **Publication-ready figures** — Well-labeled axes, legends, captions\n- **Provenance tracking** — Data sources, tool versions, timestamps\n- **Computational cost** — Runtime and resource estimates provided\n\nDemo notebooks represent the highest quality tier and serve as templates for new contributions.\n\n**See also:** [Artifacts](/docs/artifacts), [Demo Walkthrough](/docs/demo-walkthrough), [Scientific Tool Library](/docs/scientific-tools)\n\n## See Also\n\n- [Principal Pars Compacta](/wiki/cell-types-principal-pars-compacta) — associated_with\n",
  "entity_type": "scidex_docs"
}

Content snapshot

{
  "content_md": "# Computational Notebooks\n\nSciDEX integrates Jupyter notebooks as first-class scientific artifacts. Notebooks provide reproducible, inspectable analyses with code, data, and visualizations all in one place.\n\n## Why Notebooks Matter\n\nTraditional scientific claims are often black boxes: \"We found X.\" Notebooks make the analysis transparent:\n- **Reproducible** — Full code and methodology visible\n- **Inspectable** — Step-by-step reasoning preserved\n- **Interactive** — Re-run with different parameters\n- **Evidence-Rich** — Figures and tables embedded in context\n\n## Notebook System\n\nSciDEX stores notebooks in the `notebooks` table and indexes them as `notebook` artifacts. Each notebook:\n- Has a unique ID and version\n- Links to parent entities (hypotheses, analyses, wiki pages)\n- Includes metadata (author, tags, quality score)\n- Can be downloaded as `.ipynb` or viewed inline\n\nCurrently: **233 notebooks** covering topics from single-cell analysis to aging pathways.\n\n## Types of Notebooks\n\n### Analysis Notebooks\nDeep-dive analyses supporting specific hypotheses:\n- Single-cell clustering and differential expression\n- Pathway enrichment analysis\n- Comparative genomics across species\n\n### Demo Notebooks\nPolished, narrative-driven notebooks for the `/demo` page:\n- SEA-AD Alzheimer's cell type analysis\n- Aging atlas comparative analysis\n- Protein-protein interaction network analysis\n\n### Tool Demonstration Notebooks\nShow how to use specific Forge tools:\n- Allen Institute data queries\n- PubMed literature pipelines\n- KEGG pathway retrieval\n\n## Accessing Notebooks\n\n### From Hypothesis Pages\nLook for \"Computational Analysis\" sections on hypothesis detail pages. Notebooks appear with:\n- Summary of analysis methodology\n- Key findings and figures\n- Download link (`.ipynb` format)\n- Inline viewer for quick exploration\n\n### From the Artifact Gallery\nBrowse all notebooks at `/artifacts`:\n- Filter by `artifact_type=notebook`\n- Search by tags (single-cell, pathway, enrichment, etc.)\n- Sort by quality score or recency\n- Preview metadata before opening\n\n### From the Demo Page\nFeatured demo notebooks at `/demo` with:\n- Guided narrative context\n- Polished, publication-quality visualizations\n- Step-by-step explanations\n- Links to related hypotheses and entities\n\n### Via API\nProgrammatic access via `/api/notebooks`:\n```\nGET /api/notebooks?parent_type=hypothesis&parent_id=abc123\nGET /api/notebooks?tags=single-cell,alzheimers\n```\n\n## Notebook Infrastructure\n\nSciDEX's notebook system is built on:\n- **Jupyter** — Standard `.ipynb` format compatible with all notebook tools\n- **SQLite storage** — Notebook metadata and provenance tracked in `notebooks` table\n- **Artifact registry** — Notebooks are first-class artifacts with IDs and links\n- **Quality gates** — Senate-enforced review before high-visibility promotion\n\n## Quest 17 Integration\n\nNotebooks are a core component of **Quest 17: Rich Artifacts and Computational Notebooks**, SciDEX's second-highest priority quest focused on making discoveries deeply inspectable.\n\nQuest 17 notebook work includes:\n- **Notebook templates** for common analyses (single-cell, pathway enrichment, comparative genomics)\n- **Real analyses** using Allen Institute data (SEA-AD, BrainSpan)\n- **Tool integration** demonstrating how Forge tools feed notebook pipelines\n- **Quality standards** ensuring notebooks are reproducible and well-documented\n\n## Featured Notebook Examples\n\n### SEA-AD Single-Cell Analysis\n- **Dataset:** 2.3M cells from human brain tissue (Allen Institute)\n- **Analysis:** Differential expression in Alzheimer's disease vs. control\n- **Tools:** scanpy, anndata, pandas, matplotlib, seaborn\n- **Findings:** Cell-type-specific changes in microglia and excitatory neurons\n- **Link:** Available from TREM2, CD33, and APOE hypothesis pages\n\n### Aging Pathway Enrichment\n- **Dataset:** Gene expression across human, mouse, worm, fly lifespan\n- **Analysis:** Conserved aging pathway enrichment using KEGG/Reactome\n- **Tools:** gprofiler, enrichr, pathway APIs\n- **Findings:** mTOR, autophagy, and mitochondrial pathways conserved across species\n- **Link:** Available from aging-related hypothesis and mechanism pages\n\n### Protein-Protein Interaction Networks\n- **Dataset:** STRING database interactions for neurodegeneration genes\n- **Analysis:** Network clustering and hub gene identification\n- **Tools:** networkx, STRING API, community detection algorithms\n- **Findings:** APOE, MAPT, SNCA form a highly connected subnetwork\n- **Link:** Available from protein interaction hypothesis pages\n\n## Creating Notebooks\n\nForge agents generate most notebooks during analysis workflows. The process:\n1. **Analysis trigger** — Hypothesis or gap requires computational evidence\n2. **Tool execution** — Forge agent runs scientific tools (Allen data, PubMed, pathways)\n3. **Notebook generation** — Results formatted into narrative `.ipynb` with code + figures\n4. **Artifact registration** — Notebook saved to `notebooks` table and linked to parent\n5. **Quality review** — Senate checks reproducibility and documentation quality\n6. **Publication** — Approved notebooks appear on hypothesis pages and artifact gallery\n\nHuman contributors can also submit notebooks via the contributor system (see [Contributing](/docs/contributing)). All submitted notebooks undergo the same quality review process.\n\n## Notebook Quality Standards\n\nHigh-quality SciDEX notebooks include:\n- **Clear narrative** — Each cell has explanatory markdown\n- **Reproducible code** — Dependencies specified, data sources documented\n- **Publication-ready figures** — Well-labeled axes, legends, captions\n- **Provenance tracking** — Data sources, tool versions, timestamps\n- **Computational cost** — Runtime and resource estimates provided\n\nDemo notebooks represent the highest quality tier and serve as templates for new contributions.\n\n**See also:** [Artifacts](/docs/artifacts), [Demo Walkthrough](/docs/demo-walkthrough), [Scientific Tool Library](/docs/scientific-tools)",
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}