By name: pvl-peleg-review description: Peleg review task management. Use when user mentions Peleg, review tasks, fibril formation, FF data, chunk work, threshold controls, terminology scan, or any task from the holistic review document. user-invocable: true argument-hint: [chunk-number]
Peleg Review Task System
Source Document
docs/active/PELEG_REVIEW_TASKS.md — Read this FIRST for any Peleg-related work.
Workflow Protocol (MANDATORY)
- PLAN MODE FIRST — before touching any code
- ASK QUESTIONS — if ANY item is ambiguous, stop and ask. Do not guess intent.
- Research before deciding — items marked
[DECIDE AFTER RESEARCH]require web search + codebase analysis + user approval - Chunk execution — do ONE chunk per session. Summarize at end.
- FF-everywhere check — for EVERY UI element you touch: "Should FF data also be shown here?"
The Four Core Data Categories
- SSW — Switching peptides (from TANGO)
- α-Helix — Helix predictions (from S4PRED)
- FF α-Helix — Fibril-forming helical (μH/hydrophobicity thresholds)
- FF SSW — Fibril-forming switching (biochemical thresholds)
Cross-Cutting Rules (apply to EVERY change)
- FF Data Everywhere: Ask "Should FF data also be shown here?" for every UI element
- Aggregation Trust: TANGO aggregation is SECONDARY. Not in dashboard summaries, not as primary chart metrics. OK in peptide detail pages.
- User-as-Stupid Principle: Every UI must pass "would a confused first-time user understand this in 3 seconds?"
- Repetitiveness Guard: FF data everywhere relevant BUT each view shows it in the way most useful for THAT context
Chunk Summary
| Chunk | Topic | Priority |
|---|---|---|
| 1 | FF Data Layer — new columns, 4 categories, thresholds | Phase 1 |
| 2 | Threshold Controls — remove old, add smart flagging | Phase 2 |
| 3 | Terminology & UX — simplify for non-researchers | Phase 3 |
| 4 | Graphs & Visualizations — delete/replace/add | Phase 4 |
| 5 | Results Table & Filtering — FF categories in filters | Phase 3 |
| 6 | Candidate Ranking — deep research + redesign | Phase 5 |
| 7 | Peptide Detail Page — feature comparison, sliding windows | Phase 6 |
| 8 | Parked Items — compare 5+ tables, UI redesign, VM/K8s | Later |
| 9 | Cross-Cutting Concerns — FF everywhere, agg trust, UX | Always |
Starting a Chunk
If user says "chunk N" or provides $ARGUMENTS:
- Read the specific chunk from
docs/active/PELEG_REVIEW_TASKS.md - List ALL questions and ambiguities before writing code
- For
[DECIDE AFTER RESEARCH]items: search web, analyze codebase, present findings - Get user approval on the plan
- Implement
- Summarize: files changed, verification commands, what's next
Terminology Quick Reference
- "species" → "organisms" (across all UI)
- "SSW negative" / "SSW-" → "No SSW"
- "SSW positive" / "SSW+" → "SSW"
- "FF SSW" → "Fibril Forming SSW" (where space allows, or use legend)
- "15aa" → "15 amino acids" (spell out for non-researchers)