SciDEX — Task: [Exchange] Add protocols to 10 experiments

IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists. 64 experiments lack detailed protocols. Add methods, controls, expected outcomes, success criteria. ## 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 (7)

[Exchange] Verify protocols populated; task complete [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-16

[Exchange] Update spec work log with 10 more experiments enriched [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

[Exchange] Add protocols to 10 more experiments with shortest protocols [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

[Exchange] Verify protocols populated; no missing data found [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

[Exchange] Update spec work log with regression fix [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

[Senate] Fix regression: restore get_db() at wiki-quality endpoints [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

[Exchange] Add protocols to 10 experiments with shortest protocols [task:f6d9d091-e0e9-41ab-81e6-8f989ac1a848]2026-04-10

Spec File

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

☑ All experiments with missing protocols have protocol, expected_outcomes, and success_criteria fields populated

☑ Protocols include methods, controls, and analysis steps appropriate to the experiment type

☑ Expected outcomes include quantitative predictions

☑ Success criteria are specific and measurable

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

Payload JSON

{
  "requirements": {
    "coding": 8,
    "reasoning": 8,
    "analysis": 8
  },
  "_reset_note": "This task was reset after a database incident on 2026-04-17.\n\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\ncorruption. Some work done during Apr 16-17 may have been lost.\n\n**Before starting work:**\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\n\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\nSCIDEX_DB_BACKEND=postgres env var.",
  "_reset_at": "2026-04-18T06:29:22.046013+00:00",
  "_reset_from_status": "done"
}