[Exchange] Add protocols to 10 experiments

Goal

Add detailed protocol content (methods, controls, expected outcomes, success criteria) to experiments that lack them. At task claim time, 7 test experiments (all TREM2 KO amyloid pathology studies in 5xFAD/TREM2-/- mice) were missing all three protocol fields.

Acceptance Criteria

Approach

Identify experiments missing protocol/expected_outcomes/success_criteria

For each experiment, generate scientifically grounded protocol content based on experiment_type, target_gene, disease, model_system

Update the database directly via Python

Verify all fields populated

Dependencies

None

Dependents

None

Work Log

2026-04-10 — Slot 2 (f6d9d091-e0e9-41ab-81e6-8f989ac1a848)

• Re-verified: all 352 experiments have protocol, expected_outcomes, and success_criteria populated
• Verified via direct DB query to postgresql://scidex: protocol NULL=0, expected_outcomes NULL=0, success_criteria NULL=0
• Confirmed 7 exp_test_* experiments (the originally-missing ones) have 2426-char protocol strings
• Task was completed by Slot 1 agent; no additional data changes needed
• Result: Done — no missing protocols found, work already completed

2026-04-06 — Slot 1

• Found 7 test experiments (exp_test_*) all with title "TREM2 KO amyloid pathology study" missing protocol fields
• All: validation type, TREM2 target, Alzheimers Disease, Mouse (5xFAD/TREM2-/-) model
• Added comprehensive protocol, expected_outcomes, and success_criteria to all 7
• Result: Done — 7 experiments enriched with protocols

2026-04-10 14:15 PT — Slot 54 (this worktree, continued)

• Verified 10 experiments were already enriched in commit d65e3619
• Identified 10 new experiments with shortest protocols (<100 chars) not yet enriched
• Created enrichment/enrich_short_protocols_batch2.py with scientifically grounded protocols
• Added detailed protocols (2.4-3.1K chars each) for:

- APOE4 association with TDP-43 pathology in AD
- PGC-1α knockout effects on PV+ interneuron maturation
- Gene expression validation in apoE-/- mice
- Ingenuity Pathway Analysis of miR-130a target interactions
- In vivo neuronal migration assay with MAP6 depletion
- Analysis of IBA1 low/negative microglia in liver disease
- Cognitive impact of TDP-43 pathology in AD patients
- DDR factor depletion and focus formation analysis
- E2F coordination of G2/M transcriptional program
- ADCY8 regulatory mechanism investigation

• Verified API healthy (analyses=188, hypotheses=333) and all pages return 200
• Pushed to orchestra/task/78a4124c-817e-4e26-8c96-693ade19cb9b
• Result: Done — 10 more experiments enriched with comprehensive protocols

2026-04-16 — Verification (f6d9d091-e0e9-41ab-81e6-8f989ac1a848)

• Verified via direct DB query to postgresql://scidex:

- Total experiments: 623
- Missing protocol: 0
- Missing expected_outcomes: 0
- Missing success_criteria: 0

• Confirmed branch is up to date with origin/main (no diff)
• Task is complete: all experiments have protocols populated
• Result: Done — task already completed and merged to main

2026-04-16 — Current session (Slot 74)

• Discovered that while NULL/empty protocol count is 0, 111 experiments still had

placeholder protocols (< 100 chars, e.g., "Updated protocol for exp-xxx")

• Identified 10 experiments with shortest placeholder protocols for enrichment
• Created enrich_protocols_batch3.py with scientifically grounded protocols for:

1. exp-ca9ab7f0: qPCR/western blot BBB protein analysis in APP/PS1 mice (3139 chars)
2. exp-96dbc4e0: Transcriptomic profiling in AD mouse model (2729 chars)
3. exp-17c7128a: Optic nerve myelination in Gabra1/Gabrg2 mutants (2546 chars)
4. exp-4e462be7: Endothelium-specific TBK1 knockdown in atherosclerosis
5. exp-a76a5406: Irisin effects on angiogenesis in HUVECs
6. exp-f3deebc7: TBK1-PAK1IP1-PAK1 signaling pathway analysis
7. exp-ca7e1e3a: TLR4 activation assay with NETs and anti-CarP antibodies
8. exp-18b204f5: GSK8612 treatment in atherosclerosis model
9. exp-6494a58a: P2rx7 congenic mouse insulin tolerance testing
10. exp-84c87be2: Osteoclastogenesis enhancement assay (3349 chars)

• Each protocol includes: methods, controls, expected outcomes (quantitative), success criteria
• Database verified: 10 experiments now have 2500-3350 char protocols
• Committed to orchestra/task/fd1a3168-add-protocols-to-10-experiments
• Result: Done — 10 experiments enriched with comprehensive protocols

Tasks using this spec (1)

[Exchange] Add protocols to 10 experiments

File: fd1a3168_add_protocols_experiments_spec.md

Modified: 2026-05-01 20:13

Size: 4.8 KB