[Forge] A17.2: Create Jupyter Notebook Template for Allen Data Analysis done analysis:8 coding:7 reasoning:7

Build reusable Jupyter notebook template for analyzing Allen Institute datasets with SciDEX integration. Goal: Provide standardized framework for agents to generate analysis notebooks with proper structure, visualizations, and provenance tracking. Deliverables: 1. Create notebooks/allen_analysis_template.ipynb with sections: - Metadata (analysis_id, dataset, author, timestamp) - Data loading (AllenSDK queries, caching) - Exploratory analysis (cell counts, QC metrics) - Differential expression (DESeq2/Scanpy statistical tests) - Visualization (heatmaps, volcano plots, UMAP/tSNE) - Pathway enrichment (Reactome/KEGG via gseapy) - Hypothesis generation (link to SciDEX hypotheses table) - Export results (KG edges, evidence for hypotheses) 2. Include utility functions: - fetch_allen_data(dataset_id, gene_list) - differential_expression(counts_matrix, metadata, groups) - plot_heatmap(expr_data, genes, cell_types) - pathway_enrichment(gene_list, organism='human') - export_to_scidex_kg(source, target, relation, evidence) 3. Store in notebooks/ directory 4. Add notebook metadata schema to database: - notebooks table: id, analysis_id, filename, created_at, cell_count - notebook_cells table: id, notebook_id, cell_type, code, output 5. Create /api/notebooks/{analysis_id} endpoint to list notebooks 6. Add notebook link to analysis detail pages Dependencies: Install jupyter, nbformat, AllenSDK, scanpy, gseapy if not present. Test: Run template on small dataset, verify outputs, check DB insertion works. This is Quest 17 (Rich Artifacts) priority - enables all future Allen data analyses to produce rich computational notebooks. ## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Git Commits (2)

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  "completion_shas_checked_at": "2026-04-14T03:09:24.747817+00:00"
}

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