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proteinfoldingengine / WetLabEngine

GitHub catalog

Public packages under Tmp/TOE plus the protein-audit root. Summaries are editorial readings of READMEs and threads — open the GitHub tree for the runnable source. The wiki stub page is a pointer, not a second census.

  • WetLabEngine (root)

    White-box protein-simulation audit engine. JSON science contract, deterministic checks, Gemini qualitative review, Markdown report. Atlas ships a stdlib smoke test against Labs/MECP2 (15/1/3, Run 5 DEVIATION). Supported

  • Labs/p53

    12-run coarse-grained p53 DBD campaign. R248Q electrostatic failure vs Y220C kinetic trap. Contact-anneal + PhiKan083 improved Y220C inside this force field. GitHub-only, Aug 2025. Restricted

  • Labs/MECP2

    19-run Rett MBD–DNA campaign. InterfaceAnneal seats R106W and R133C. Engine abstract: 15 CONFIRMED, 1 DEVIATION, 3 INDETERMINATE. GitHub-only, Aug 2025. Restricted

  • uqcf_bridge_v9_update_bundle

    Frozen v9 bridge memo plus 1UAO / 1L2Y summary CSVs. Author score 7.6/10. Backbone-ordering, not basin-selection. Restricted

  • uqcf_bridge_v9_trajectory_packet_bundle

    Raw baseline-vs-v9 traces for 1UAO and 1L2Y (RMSD, sigma_bridge, closure_ready). Posted 12 Apr 2026 for artifact checking. Restricted

  • Einstein Phase 1

    V824 Accessibility Curvature Law paper (V824). Scalar/conformal recoverability geometry. Supported

  • Einstein 2

    V831 20 May ADM-like working notes around the V831 freeze: V828–V837 momentum/Onsager/Euler–Lagrange audits plus full_stack_accessibility_flow.py. V824 the same day pruned tensor/ADM. Not a restored ADM claim. Restricted

  • Einstein 3

    V923 V923 ternary source-role handshake: geometry admits the basin; information certifies the source. Observable geometry alone 62.86%; ternary lift 100%. Finite branch, no GR claim. Restricted

  • Einstein 4

    V997 23 May Genesis Pin publication audit. Holds v996 visual proof, v997_genesis_pin_publication_audit, and V997_FULL_STACK_GENESIS_PIN_BRIDGE_REPORT.md. Same visible state is not legitimacy. Restricted

  • Einstein 5

    V1011 25 May V1011.1 certification: Ω similarity + Genesis Pin + Bianchi-like source-flow closure. v1011_1_full_certification_package and v1011_bianchi_closure_audit. Restricted

  • Einstein 6

    V1152 Late-May V1025–V1152.5 provenance stack: native continuity, Genesis Pin flow, cinematic provenance, recoverable pruning. 28 May V1152.5: Ω similarity can be faked; only provenance + ordered flow closure certifies. Restricted

  • Einstein 7

    V1472 1 Jun BPI2014 / geometry-cannot-validate-itself support. v1472_retained_bridge_support_package plus Einstein 7 working files. Scoring law M_total = C_topological × P_sequence × E_arrow. Restricted

  • Einstein 8 v1638_full_stack_retained_bridge_l123_package

    V1638 V1638 full-stack retained bridge: Genesis Pin through L1/L2/L3, synthetic hypergraphs, NMI vs pruned-history nulls. Restricted

  • Einstein 9_v1686_l3_geometry_plus_information

    V1686 V1686: L3 as geometry-plus-information — hyperedge memory target T_H and entropy-order curvature driver D_L3. Restricted

  • Einstein 10_v1687_21_l4

    V1687 V1687 L4 layer: hyper-associator / H4 residual that the atlas “final boss” refuses to project away. Public 6 Jun film + sim_l4.py. Restricted

  • Einstein 11 - V1688_holonomy_proof_visualizer_v4_package

    V1688 V1688 holonomy proof visualizer. Originally posted as directed native holonomy from recombination + L3/L4 + provenance cycles. 10 Jun 2026 audit downgraded that reading to non-reciprocal directed transport. Corrected

  • Einstein_12_V1698_valid_only_slow_atlas_closure_mp4_package

    V1698 V1698 global atlas closure package with MP4: five-chart cover, inverse/cocycle/holonomy, provenance lock. Supported

  • Einstein_13_V1720 retained_bridge_core

    V1720 V1720 retained-bridge core following atlas closure — next objects after Pillar 1. Restricted

  • uqcf_codazzi_proof

    High-precision Codazzi verification on the three-binary-node exponential family. Includes August 2026 scientific status report. Supported

  • uqcf_w_holonomy_replication

    Independent W-holonomy replication: pair-marginal BKM polar loop on generalized three-qubit W states. Supported

  • uqcf_retained_information_state_research_bundle

    Does realization require a retained-information state R_t beyond what is visible in G_t? C3++ telemetry falsifier. Open

  • UQCF_Quantum_Compatibility_Lab

    v9.167–v9.171 matched four-weight family: same pair spectra and compatibility-distance curve, global completion dimensions 315 vs 311. Computed 3D sections, collective measurement 48.03% vs 46.55%. Not the v9.156 d(t) family. Gravity not established. Restricted

  • UQCF_GEM_v12_41_PUBLIC_SIMULATION_COMPLETE

    Public 121-step qubit moment-map closure. Exact KKS identity Δ_closure=0; broken generator law Δ_closure max 0.297. Ordered relational sweep, not physical time. Restricted

  • v15.12 pre-time-to-history demonstrator

    v15.12 13 Sep 2026 X + GitHub branch. Three-qubit demo: reversible pre-time motion, supplied RAS/RCR, ordered history ROOT→101. Ranks 8→4→2→1. Middle weight ≈8.19%. 30 new + 20 preserved tests. Not a STATUS gate. Time and gravity not derived. Restricted

  • v15.13 independent-events demonstrator

    v15.13 13 Sep 2026 X + GitHub branch. Four-qubit poset demo: 96 runs, reordering incomparable events preserves state/joint weight at matching records (~10⁻¹⁵). No imposed global clock. Outcomes supplied. Not a derivation of time. Restricted

  • ResearchHistory/UQCF-GEM (v13–v14)

    v14.04 GitHub-only 12 Sep 2026 campaign. Latest completed: v14.04 intertwiner stop. v14.03 preserved conditional. Restricted: HCPR, QMAR, QRSL, RSCL. RGCL REQUIRES_NEW_AXIOM. Pillar 3 OPEN. Genesis Pin is a ledger, not a selector. Restricted

  • uqcf_gem_package 2

    UQCF-GEM package drop — visuals and supporting materials for the GEM bridge. Restricted

  • uqcf_visuals_package

    Visual pack for UQCF-GEM talks and threads. Restricted

  • uqcf_bridge_final_verification_pack

    Final verification pack for the UQCF bridge trajectory. Restricted

  • package17_bundle

    Derivation program for the GEM bridge: microscopic law, operator theorem, χ fixed point, continuum limit, FLRW + perturbations, failure modes. Open

  • ai_peer_review_bundle_v1

    Restricted affine coupling peer-review packet: Theorem Packet v27, calibration runbook, constructed-dataset results. Restricted

  • final_bridge_manuscript_and_supporting_materials

    Bridge-closure status note plus manuscript supporting files. Hierarchical selector, seams, transfer, weak ladder. Restricted

  • restricted_fractal_publication_bundle

    Restricted-fractal publication bundle and corollary notes on fractal growth of the restricted bridge. Restricted

  • battery

    NASA PCoE LCO V720 pipeline and synthetic V723/V724 recoverability assays. Supported

  • GR Work

    GR correspondence working directory. Holds the 19 May V760 AtriumSimulation.py (g_eff = Ω² g0 under recovery pressure). Computational, not a GR derivation. Open

  • Retained Atlas Program

    Program folder for retained-atlas capacity law, proofs, and animation. 11 May C_norm self-healing toy lives here as RETAINED_ATLAS_CAPACITY_LAW_REPORT.md. Restricted

  • Reachability Collapse Law

    V300 V300 Normalized Adaptive Reachability Law. A_norm = A(t)/A_baseline; collapse when A_norm < A_c ≈ 0.53–0.58. Paper + v300_reachability_collapse_law_proof.py. GitHub folder name has a trailing space. Restricted

  • Irreducible_Law

    Irreducible-layer law notes (L3/L4 cannot be projected away). Restricted

  • v1688_holonomy_review

    Review packet for the V1688 holonomy visualizer. Restricted

  • v395_full_stack_proof_kit

    V395 V395 full-stack proof kit: A_t = M_t × R_t era, before L_t. Irreducibility tests from V346–V395. Control/survival law, not GR. Restricted

  • v421_independent_validation_package

    V421 V421 blinded generalization of the recursive survival law S_t = M_t × R_t × L_t. Restricted

  • v498_retained_geometry_formal_report_package

    V498 V498 retained-geometry Python proof: C_t = M_t R_t L_t + λ0 η_convert B_t, g_eff driven by T_retained / C_surplus, six graph families. Script header: not a GR derivation. Restricted

  • v505_continuum_object_package

    V505 V505 conformal recoverability checkpoint: g_eff = Ω² g0 with weak-form Source/Repair/dμ_defect evolution. v505_weak_form_validation.py. Not a GR continuum-limit derivation. Restricted

  • v513_formal_theorem_package

    V513 V513 formal theorem package: g_eff = Ω² g0 with listed proof gaps (Ω convergence, MRL uniqueness, Lyapunov). Restricted

  • V513_gap_closure

    V513 V535 η_convert freeze: harmonic-mean channel efficiency times exp[-C_repair_min]. v513_eta_proof_harness.py. Operational/theorem-shaped; uniqueness not complete. Restricted

  • v541_final_theorem_bundle

    V541 V541 conformal recoverability flow bundle: theorem report, evidence harness, claim-boundary file. Lyapunov-supported, not a completed theorem. Restricted

  • v549_theorem_boundary_update_bundle

    V549 Boundary update after V541, immediately before the V555 adversarial harness. Not a completed theorem. Restricted

  • V555

    V555 V555 adversarial verification: selective-fragility AUC 1.0 and defect-localization AUC 1.0 on synthetic attacks (fake liquidity, scrambled defects, coordinated fake recovery). Restricted

  • V722

    V722 V722 recoverability / stress-geometry precursor to the V723/V724 assays. Restricted

  • v724_stress_test_outputs

    V724 V724 synthetic stress-test: overlapping k, reserve fatigue, aliased windows. adm_z AUC 1.000 → ~0.845; passive burden stays near chance. Restricted

  • v925_source_role_closure_hardening

    V925 Source-role closure hardening — provenance/source gates. Restricted

  • Sparc_runner

    SPARC rotation-curve runner used in holdout / external-validation challenges. Restricted

  • great_grok_challenge_bridge_sparc_holdout_pack

    First Great Grok Challenge real-data pack: SPARC holdout (NGC 2403 / 3198 / 6503) for the frozen Bridge. Restricted

  • things_ngc2403

    NGC 2403 working materials — galaxy-scale holdout object. Restricted

  • bridge_dark_sector_proxy_output

    Dark-sector proxy outputs from the bridge program. Open

  • ThePhysicsParadox

    Notes on the physics paradox framing (motion/gravity before time; entropy as observation). Restricted

  • Mouse

    Mouse / recoverability working directory. 16 Jun 2026 public sim: a pruning network experienced as time; six posted code–universe isomorphisms. Restricted

  • quantum_bridge_supporting_materials

    Supporting materials for the quantum-side of the GEM bridge. Restricted

  • fresh_retained_state_confirmation_bundle

    Confirmation bundle for the retained-information state. Restricted

  • dual_activation_direct_calibration_bundle

    Direct calibration bundle for dual-activation models. Restricted

  • challenge14_packet

    Challenge 14 external-pressure packet — frozen SPARC 171 pass. Restricted

  • post_ready_bundle_v1

    Post-ready communication bundle v1. Restricted

  • retained_core_conditional_context_packet_bundle

    Conditional-context packet for the retained core. Restricted

  • round10_external_validation_bundle

    Round 10 external validation bundle. Restricted

  • round10b_downloads

    Round 10b download artifacts. Restricted

  • Round11

    Round 11 working directory. Restricted

  • round12

    Round 12 working directory — WALLABY unseen transfer. Restricted

  • round13

    Round 13 working directory — conditional win / holdout. Restricted

  • Round15

    Round 15 skeptic’s challenge — clusters and lensing. Restricted

  • Round16

    Round 16 widened cluster set; last empirical round before Package 17. Restricted

  • bridge_repro_sequence_rounds_3_to_6

    Reproduction sequence for bridge rounds 3–6. Restricted

  • bridge_round9_results

    Bridge round 9 results drop. Restricted

  • weak_frontier_supporting_documents_bundle

    Weak-frontier supporting documents (lower ladder / weak coupling). Restricted

  • Prediction_curve_beta

    Prediction-curve beta — applied forecasting overlay. Restricted