BioNexus v1.0.0-rc.5 (Release Candidate 5)

BioNexus v1.0.0-rc.5 — Release Candidate 5

This release establishes empirical lab readiness, introduces the automated Differential Expression (DE) Audit Engine with PI Decision Items, external scientific connector profiles, cluster stability quantification, and a complete cryptographic Evidence Index.

Key Highlights & Capabilities

• Differential Expression Audit Engine (bionexus.de_audit, BFA-001/003):
  • Scans single-cell DE results and expression matrices for pseudoreplication signatures (tiny p-value inflation $p < 10^{-100}$), missing FDR corrections, donor representation skew, and unmodeled batch confounding.
  • Automatically generates actionable PI Decision Items with concrete trade-off rationale and drop-in minimal fixes.
• Cluster Stability & Perturbation Robustness (bionexus.clustering_stability):
  • Validates single-cell clustering stability across cell subsamplings, resolution sweeps, and random seeds (ARI & NMI metrics).
• External Scientific Connector Profiles (BNS-025):
  • Standardized connector profile specifications under standards/connector-profiles/ for bioRxiv, ChEMBL, Consensus, Enrichr, OpenTargets, Owkin, and PubMed.
  • Generates tamper-evident execution receipts and enforces fail-closed claim boundaries.
• Cryptographic Evidence Index & Epistemic Lineage (bionexus.evidence_index, validation/EVIDENCE_INDEX.json):
  • Cryptographically indexes and hash-verifies 53+ empirical validation artifacts, flagship reports, and benchmark datasets.
  • Ensures deterministic provenance tracking between source rules, validation artifacts, and research claims.
• Independent Validation Network (IVN) & BNS-019 Interoperability:
  • TypeScript SDK and client validator for the BNS-019 trial protocol (interoperability/bns019/typescript/).
  • Zero-touch CI verification and strict empirical validation quota enforcement.
• Unified SSOT Alignment:
  • Full version agreement across all 10 platform manifests and distribution packages with 1,322 passing unit tests.