[Artifacts] Jupyter notebook template for Allen Brain analysis

[Artifacts] Jupyter notebook template for Allen Brain analysis

Goal

Create a comprehensive Jupyter notebook template for analyzing Allen Brain Atlas data. The template will serve as a starting point for neuroscience researchers to query the Allen Brain API, extract gene expression data, perform statistical analysis, and visualize results. This supports the Atlas layer by providing reproducible analysis workflows linked to the knowledge graph.

Acceptance Criteria

Approach

Create notebooks/ directory if it doesn't exist

Build Jupyter notebook with sections:

- Introduction and setup (AllenSDK installation)
- Allen Brain API queries (brain-map.org)
- Gene expression data extraction
- Data visualization (matplotlib, seaborn)
- Statistical analysis (differential expression with scipy)
- Pathway enrichment (Enrichr API integration)
- Summary and next steps

Test notebook structure is valid JSON

Update work log with completion details

Commit and push changes

Work Log

2026-04-02 09:44 UTC — Slot 4

• Started task: Create Jupyter notebook template for Allen Brain analysis
• Created spec file following AGENTS.md format
• Created notebooks/ directory at /home/ubuntu/scidex/notebooks/
• Built comprehensive Jupyter notebook template with:

- Section 1: Environment Setup (AllenSDK installation, imports, plotting config)
- Section 2: Allen Brain API queries (query_gene_expression function, ISH experiments)
- Section 3: Gene expression extraction (structure tree, expression matrix extraction)
- Section 4: Data visualization (heatmaps, bar plots, distribution plots with matplotlib/seaborn)
- Section 5: Differential expression analysis (t-tests, ANOVA, volcano plots with scipy)
- Section 6: Pathway enrichment (Enrichr API integration for KEGG, GO, WikiPathways)
- Section 7: Summary and next steps (export to JSON, resources)

• Notebook structure validated: 22 cells (8 markdown, 14 code), nbformat 4.4
• All acceptance criteria met:

- ✓ Jupyter notebook created at notebooks/allen_brain_template.ipynb
- ✓ AllenSDK setup and installation instructions
- ✓ brain-map.org API query examples
- ✓ Gene expression data extraction and preprocessing
- ✓ Basic visualizations (matplotlib/seaborn)
- ✓ Differential expression analysis (scipy t-tests, ANOVA)
- ✓ Pathway enrichment analysis (Enrichr API)
- ✓ Well-documented cells with markdown explanations
- ✓ Code follows best practices (error handling, type hints, clear variable names)
- ✓ Notebook structure validated successfully

• Result: Complete - Ready for researchers to use for Allen Brain analysis workflows

Already Resolved — 2026-04-24 15:35:00Z

Verification Evidence

• Checked origin/main:notebooks/allen_brain_template.ipynb — notebook exists with 22 cells (8 markdown, 14 code), nbformat 4.4
• All acceptance criteria verified present in main:

- ✓ AllenSDK setup (allensdk imports in cell 3)
- ✓ brain-map.org API queries (api.brain-map.org URL in code)
- ✓ Gene expression extraction (expression handling in cells 7-8)
- ✓ matplotlib/seaborn visualization (heatmap, bar plots in cells 10-12)
- ✓ Differential expression with scipy (ttest_ind, f_oneway in cells 14-16)
- ✓ Enrichr pathway enrichment (enrichr_submit_genes, enrichr_get_results in cells 18-19)

• allen_analysis_template.ipynb also exists on main as alternative (33 cells)
• Commit 698ed86b2 on main introduced the allen_brain_template.ipynb (from task d16-05-7)
• Task acceptance criteria already satisfied — closing as done.

[task:a17-02-87C1C845]

File: a17-02-87c1c845_artifacts_jupyter_notebook_spec.md

Modified: 2026-04-24 08:34

Size: 4.7 KB