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Archive v1.0 milestone: 6 phases, 21 plans, 40/40 requirements. Reorganize ROADMAP.md, evolve PROJECT.md, archive requirements. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Milestones
v1.0 MVP (Shipped: 2026-02-12)
Phases completed: 6 phases, 21 plans Lines of code: 21,183 Python (src + tests) Files: 164 files Timeline: 2026-02-11 → 2026-02-12
Delivered: Reproducible bioinformatics pipeline that screens ~20,000 human protein-coding genes across 6 evidence layers to identify under-studied cilia/Usher syndrome candidate genes, with transparent weighted scoring, tiered output, and comprehensive validation.
Key accomplishments:
- Reproducible data foundation with Ensembl gene universe, validated HGNC/UniProt mapping, Pydantic config, DuckDB checkpoint-restart, and provenance tracking
- 6-layer evidence integration: gnomAD constraint, tissue expression, gene annotation, protein features, subcellular localization, animal models, and PubMed literature
- Transparent weighted scoring with NULL-preserving composite scores, configurable per-layer weights, and quality control (missing data rates, distribution anomalies, MAD outliers)
- Tiered candidate output (high/medium/low confidence) with dual-format export (TSV+Parquet), visualizations, and reproducibility reports
- Comprehensive validation: positive controls (recall@k), negative controls (13 housekeeping genes), sensitivity analysis (weight perturbation with Spearman rank correlation)
- Unified CLI with 5 subcommands (setup, evidence, score, report, validate) and consistent checkpoint-restart pattern
v2 requirements delivered early:
- Sensitivity analysis with parameter sweep (ASCR-03)
- Negative control validation with housekeeping genes (AOUT-02)
Archive: v1.0-ROADMAP.md | v1.0-REQUIREMENTS.md | v1.0-MILESTONE-AUDIT.md