Changelog

v0.5.2 (2026-05-25)

Catalog schema

  • data/catalog_v0.5.2_current.parquet: two new boolean columns required by PEN-COMPARE v3.2. intrinsic_cargo_mechanism is True for all 1,029 designs (all pass IS110-family PFAM triage: PF01548 and PF02371). cell_based_evidence is False for all 1,029 designs (all are computational predictions with no peer-reviewed mammalian cell data).

  • parent_editor column populated with canonical editor names.

  • scripts/upgrade_catalog_to_v052.py - reproducible catalog upgrade script.

  • 11 new tests verifying v3.2 compatibility invariants.

Dependency pins

  • genome-atlas>=0.7.2,<0.8.0, mech-class>=0.5.4,<0.6.0, pen-score>=0.1.3,<0.2.0.

Pre-registration integrity

  • All v0.5.0 pre-registration results unchanged. P1: 16 designs beat the IS621 verbatim lockpoint (0.929). Total designs: 1,029.

v0.5.1 (2026-05-24)

Dependency updates

  • pen-score>=0.1.2,<0.2.0: 8-axis PenScore with the S_Energy axis. All IS110-family designs gain S_Energy = 1.0; weight redistribution is near-neutral for IS110 designs.

  • mech-class>=0.5.3,<0.6.0 and genome-atlas>=0.7.1,<0.8.0.

Re-scoring

  • data/catalog_v0.5.1_current.parquet produced by scripts/rescore_v012.py (8-axis, pen-score v0.1.2).

  • IS621 reference lockpoint: 0.929 to 0.957. Designs beating 0.957: 2.

  • catalog/release_v0.5.0/pen_assemble_catalog.parquet (v0.5.0, 7-axis) is the frozen pre-registration record and is not modified.

Pre-registration integrity

  • The P1 prediction was tested against v0.1.0 scores: PASS, 16 designs, FINAL. The v0.1.2 lockpoint (0.957) is reported as a secondary current-best-estimate analysis only.

v0.5.0 (2026-05-20)

First public release.

Pipeline

  • Design sourcing: (1,041 designs across 4 strategies), PenScore computation, ESMFold structural predictions, MHCflurry 2.2.1 immunogenicity scoring.

  • Eight-gate triage: (1,029 survivors), bootstrap rank stability, diversity analysis, failure-mode analysis.

  • Five pre-registered formal prediction tests (all PASS).

  • Public catalog: - CSV/Parquet scorecard, FASTA files, 1,029 per-design JSONs, self-contained HTML browser, wet-lab Markdown references.

Package

  • pen_assemble.pen_score - PenScore formula, IS621 lockpoints.

  • pen_assemble.catalog - catalog loading utilities.

  • pen_assemble.codon - codon optimisation, restriction-site scanner.

  • Test suite: 63 unit tests (pytest).

  • Sphinx documentation.

Key results

  • 16 designs beat IS621 verbatim lockpoint (0.929).

  • IS621_deimmunized_v2 achieves PenScore = 0.9673.

  • 992 Strategy B IS110 orthologs pass all triage gates.

  • 5/5 pre-registered predictions PASS.

Disclosed deviations

  • Rosetta stability gate non-functional (universal, all 47 designs) - auto-passed.

  • P3 IS621 reference corrected from 0.250 to 0.7594.

  • P5 rank-5 diversity-enforced (A_007 replaces D023).

  • Gate 8 ATLAS not evaluated for Strategy B.