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51face03433df41f9972a2639b903c01e5ecfb0bebfccd36ffc04e69200d2ccf computed Detailed NAR methods supplement covering resource provenance, DMD signatures, HepG2 delta store, split design, CPU baselines, candidate ranking, and GPU claim boundaries. methods;supplementary_methods;reproducibility v0.1.0-20260706 results/nar_methods/NMD_VCELL_METHODS_REPRODUCIBILITY_MATRIX.tsv yes methods public_ready 2713 8389b1fcad179f7970d9418a578f22c62be92f88385aa9fac0533c399affe0d6 computed 8 Method-block reproducibility matrix with evidence files, dynamic statistics, claim boundaries, and manuscript destinations. methods;supplementary_data;reproducibility v0.1.0-20260706 results/nar_methods/NMD_VCELL_METHODS_READINESS_SUMMARY.json yes methods public_ready 572 6479421346671e91f0ed0599ce4688d8a5292a5c0ef7d7dbe98d3cbd0b634966 computed Machine-readable methods readiness summary including delta-store dimensions, split counts, candidate tiers, and method-block status. methods;resource_dashboard;reproducibility v0.1.0-20260706 results/nar_methods/NMD_VCELL_DETAILED_METHODS_PACKAGE_INDEX.md yes methods public_ready 552 0c7a67f95f34896df4cb67a2999871c91944161e039847c46e91b195d812db07 computed Index for detailed methods supplement, reproducibility matrix, and readiness summary. methods;supplementary_data v0.1.0-20260706 results/remote_dmd_signatures/human_filtered_dmd_gene_consensus_signature.tsv yes disease_signature public_ready 6687630 47e42705e667704f3f4d6d40bd6d00b7f9b68e885e89a1979380fcba52ea89cc computed 17919 Human-gene-filtered DMD consensus disease signature. figure_2;supplementary_data v0.1.0-20260706 results/remote_dmd_signatures/human_filtered_dmd_context_signatures_top100.tsv yes disease_signature public_ready 216663 235c6109a3b89afc29a4dd54fcfc3c344237b6e7d1473f76d8f80560b8d77fd6 computed 783 Top context-specific DMD signature genes. figure_2;supplementary_data v0.1.0-20260706 results/remote_dmd_signatures/human_filtered_dmd_signature_gene_sets.gmt yes disease_signature public_ready 10367 34dfa693adb7fcdc39173a498a4c5314d096d5f03d080f6c8a59db30686394a4 computed DMD signature gene sets in GMT format. supplementary_data v0.1.0-20260706 results/prjna772047_patient_muscle_delta/disease_vs_control_delta.tsv yes external_validation public_ready 4500181 d3806f14e1f5a5cb862b674b0ddf534ab7605db1faf23b4a3d0aebfcc8c0f361 computed 36591 Human patient muscle disease-vs-control pseudobulk delta. figure_2;supplementary_data v0.1.0-20260706 results/prjna772047_patient_muscle_delta/prjna772047_delta_vs_remote_dmd_signature.summary.tsv yes external_validation public_ready 589 036ade8b41066748f0d54d2fa9650f0ecb1969022da63048af9b29cac1bfde78 computed 1 Patient muscle delta against DMD signature summary. figure_2 v0.1.0-20260706 results/dmd_organoid_signature/dmd_vs_control_signature.tsv yes external_validation public_ready 4641529 87814570695088d05e5822668edb0301dddbafcff5cf8377fd56db3c9d76094f computed 36601 DMD organoid/model disease-vs-control signature. figure_2;supplementary_data v0.1.0-20260706 results/dmd_organoid_signature/DMD_ORGANOID_SIGNATURE_SUMMARY.md yes external_validation public_ready 4406 704d8e35e2f6615d505346d73e6c2649072c3b0e57593131323a320326be517d computed DMD organoid signature summary. figure_2 v0.1.0-20260706 results/cell_state_resolved_validation/CELL_STATE_RESOLVED_VALIDATION_REPORT.md yes external_validation public_ready 7181 e40f41b2cf9e7ed4a4f67fdc516e1ac6a65f57a303f575bb94920795e3c656a3 computed Cell-state-resolved DMD signature validation report. figure_2;supplementary_data;model_selection v0.1.0-20260706 results/cell_state_resolved_validation/CELL_STATE_VALIDATION_GATE.md yes external_validation public_ready 3346 b09e68d3507b48e0ab90dcdb8c2c676f04da9b82afcf3a553b2e101821c3f7ab computed Cell-state validation gate report for source-supported DMD-aligned contexts. figure_2;supplementary_data;model_selection v0.1.0-20260706 results/cell_state_resolved_validation/cell_state_validation_gate.tsv yes external_validation public_ready 6139 baf110e3e5584934983f0d8b239ea7fbc5fb0ec6e145f37f8758597bc2221b12 computed 28 Machine-readable cell-state validation gate for DMD signature alignment. figure_2;supplementary_data;model_selection v0.1.0-20260706 results/cell_state_resolved_validation/cell_context_dmd_signature_scores.tsv yes external_validation public_ready 20476 29d97f89626f95e8e3288ed3af94cb874f7a72462cd646c4f839b2af9718158d computed 58 Cell-context DMD signature alignment scores across source tables. figure_2;supplementary_data;model_selection v0.1.0-20260706 results/cell_state_resolved_validation/cell_context_top_alignment_contributors.tsv yes external_validation public_ready 1086306 bb9da85815150e3ed0569df715a37fe2354f5f575ee17358af42fe91556f7d8d computed 5800 Top aligned and opposing genes contributing to each cell-context DMD alignment score. figure_2;supplementary_data;interpretation v0.1.0-20260706 results/state_nadig_trade_actual/delta_store/hepg2_trade_hvg_delta_store_manifest.json yes perturbation_resource public_ready 902 3bed824447078eb22b8a7bc2e3162310a05a0d18650359ec4d94fcfd5690dc2d computed Manifest for the cached HepG2 TRADE perturbation delta store. figure_3;methods v0.1.0-20260706 results/state_nadig_trade_actual/delta_store/hepg2_trade_hvg_delta_store_hvg_features.tsv yes perturbation_resource public_ready 53616 83788f88da60563dabaccb4972c5543b8dc4405abd0e62d1f30f4a2fa12f8c4a computed 2000 HVG features used for the HepG2 perturbation delta store. methods;supplementary_data v0.1.0-20260706 results/state_nadig_trade_actual/delta_store/hepg2_delta_neighbor_index_summary.tsv yes perturbation_resource public_ready 20216 3df0cc1076ed5f868b743ec3e46dc19ab13693f416bb1b39f3d7420342a9ed5e computed 99 Perturbation-delta neighbor summary for target interpretation. figure_5;supplementary_data v0.1.0-20260706 results/state_nadig_trade_fewshot/hepg2_fewshot_split_manifest.tsv yes benchmark public_ready 3679 1acd71f69b05425d19aa8a9ef729e4b1504c2e67b8f625204012e548d7b6c57d computed 41 Few-shot train/validation/test perturbation split. figure_3;methods v0.1.0-20260706 results/run_comparisons/cpu_20step_validation_gate.tsv yes benchmark public_ready 533 a32865466b3534e06b9e82872b58c2164df53627f0de2e3060fd9a933a93b8ff computed 2 CPU 20-step STATE validation gate. figure_3;table_2 v0.1.0-20260706 results/run_comparisons/cpu_20step_candidate_gate.tsv yes benchmark public_ready 367 001fbf3546f5f2013c9419452f14bbf18b5be87cc7eb5b41464dc5a1a28ffd61 computed 1 CPU 20-step candidate screen gate. figure_3;table_2 v0.1.0-20260706 results/cpu_baselines/hepg2_classical_baselines_cpu_rescue_cv_summary.tsv yes benchmark public_ready 192 52713ffa93598db7f73be145dec6eb2f358be0a1cc16e5882a60439493da1841 computed 1 Ridge rescue-score cross-validation summary. figure_3;table_2 v0.1.0-20260706 results/cpu_baselines/hepg2_classical_baselines_cpu_validation_delta_summary.tsv yes benchmark public_ready 2531 c37722a5718d1d32d921dcca204b634d92072165cf80ea7da7dca0b88a93e6a4 computed 16 Deployable delta baseline validation summary. figure_3;table_2 v0.1.0-20260706 results/cpu_baselines/hepg2_classical_baselines_cpu_candidate_classical_rank.tsv yes candidate_prioritization public_ready 41217 4870327e66d8a475fa52ce4fa9df444579dbad8d1dd9d1d1440c6e514ffac60f computed 58 Classical candidate consensus ranking. figure_4;table_3 v0.1.0-20260706 results/decision_support/hepg2_candidate_decision_matrix_cpu_20step.tsv yes candidate_prioritization public_ready 74895 4aae9e4ba05c5e89553f5a4ced1f761e68448aab307d228fd9e6dbbfa9628c43 computed 58 Decision matrix integrating observed, model, safety, and neighbor evidence. figure_4;table_3 v0.1.0-20260706 results/state_nadig_trade_actual/hepg2_candidate_screen_queue_v3_classical_manifest.tsv yes candidate_prioritization public_ready 7063 560f998cc7a4e8e4d5c5b5a65aedfd51fa0d0f3422dc963fd7edb3e5534aab1e computed 21 GPU-ready candidate queue v3. figure_4;table_3;gpu_runbook v0.1.0-20260706 results/neuromuscular_gene_coverage/neuromuscular_gene_hepg2_trade_coverage.tsv yes scope_boundary public_ready 7483 6b7bb296841147dba2e13094776180b46c519ae120a79ba3e55afd8c863b759d computed 64 Neuromuscular sentinel gene coverage in HepG2 TRADE. figure_5;limitations v0.1.0-20260706 results/nmd_scope_extension/nmd_scope_extension_matrix.tsv yes scope_boundary public_ready 16157 9a1ed11552c7d96aceda43a4633078e60e9fe8fe32c8f86c2df8259587f47f59 computed 64 Gene-level NMD scope and claim-boundary matrix. figure_5;limitations v0.1.0-20260706 results/nmd_scope_extension/nmd_scope_extension_family_summary.tsv yes scope_boundary public_ready 651 a01574def1dd678dc017c331f77881a1c31dd3a91954fa27c98ceb6689e59d09 computed 6 Disease-family NMD scope summary. figure_5;limitations v0.1.0-20260706 results/nmd_scope_extension/NMD_SCOPE_EXTENSION_REPORT.md yes scope_boundary public_ready 1684 c6b93a18f58c199e3b1d4e64a6e3b523146f4fb802bcc99bc5b206510ea76601 computed Narrative NMD scope-extension boundary report. figure_5;limitations v0.1.0-20260706 results/neuromuscular_gene_coverage/neuromuscular_gene_hepg2_trade_neighbors.tsv yes scope_boundary public_ready 4306 da6b0acf986e05392d4d8512e4fc4d6a6b0509492a87a065e8a526802d629f94 computed 80 Delta-neighbor support for neuromuscular sentinel genes. figure_5;supplementary_data v0.1.0-20260706 reports/NEXT_GPU_RUNBOOK.md yes gpu_protocol public_ready 10093 8a04cf62989eb34777715517d7d28ba8f572055656048f40728e0beaa4726b0e computed GPU execution runbook. methods;future_gpu v0.1.0-20260706 results/gpu_strategy/hepg2_gpu_preflight_metric_gates.tsv yes gpu_protocol public_ready 2923 a002ee3e858b1e8376a4e1cae780d40cb6137cab9c1630c3eb1aa79bd2b54a69 computed 17 Pre-registered GPU metric gates. methods;future_gpu v0.1.0-20260706 results/gpu_strategy/hepg2_gpu_preflight_training_matrix.tsv yes gpu_protocol public_ready 1170 a21ea073ee2ef20127ef85fe73556ee2347263754a77fbccbc5800f27350d205 computed 5 GPU run matrix. methods;future_gpu v0.1.0-20260706 results/gpu_strategy/GPU_AUTORUN_STATUS.md yes gpu_protocol public_ready 3356 f35522eb558a13a0bd74629552b108bab1f36f8a0b11b9ad74bdb0d299e5b8eb computed GPU autorun readiness report and next command. methods;future_gpu;operations v0.1.0-20260706 results/gpu_strategy/gpu_autorun_status.tsv yes gpu_protocol public_ready 2033 7e4787f76bcc1f5a138b087dc6de96f5a53c5f5fed40774e64fcbebd2535cbaf computed 25 Machine-readable GPU autorun readiness checks. methods;future_gpu;operations v0.1.0-20260706 results/gpu_strategy/gpu_autorun_status.json yes gpu_protocol public_ready 623 99d546f3eabe4eef84b4e16b0cfbca85676209d4f2aa0af74b39f42b2a87d070 computed Structured GPU autorun readiness payload. methods;future_gpu;operations v0.1.0-20260706 results/gpu_strategy/gpu_autorun_last_submission.tsv yes gpu_protocol public_ready 208 959743411d88fa998fc88433ae9230b2a19a48437000178a66bc4c7f687c0bcd computed 1 Last GPU autorun submission record when available. future_gpu;operations v0.1.0-20260706 results/gpu_strategy/POST_GPU_REFRESH_STATUS.md yes gpu_protocol public_ready 2754 c3639af1540900de0446b10ae782279180a81332eaca4eb60ad634a8b7aff780 computed Post-GPU refresh report for NAR tables, portal, and release files. future_gpu;operations;manuscript_refresh v0.1.0-20260706 results/gpu_strategy/post_gpu_run_inventory.tsv yes gpu_protocol public_ready 803 2ff79b8597bd6c7282a081cde2e6b01a5bd23c064ff217db518cc0692402b7d3 computed 1 Inventory of completed GPU run outputs discovered by the post-GPU refresher. future_gpu;operations;manuscript_refresh v0.1.0-20260706 results/gpu_strategy/post_gpu_expected_artifacts.tsv yes gpu_protocol public_ready 1892 3943509116641f2baf8f0b4d0c243680960dbfe7fc1da308819dbb82fb2ec9f3 computed 11 Expected artifact checklist for the selected GPU run. future_gpu;operations;manuscript_refresh 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public_ready 252999 a1079fd2ff990980f83e1cb75dfe1bbd16c3c2ddf8e47e4aebb9c8134661053a computed Draft Figure 1 PNG. figure_1 v0.1.0-20260706 results/nar_figures/figure2_dmd_signature_atlas.svg yes figure public_ready 38477 53f2b94ab79f9f326c8eb4b5ac6466d6761265e96ea43793e996041a9c2af657 computed Draft Figure 2 SVG: DMD signature atlas. figure_2 v0.1.0-20260706 results/nar_figures/figure2_dmd_signature_atlas.png yes figure public_ready 291648 ec6e8bbc840399a48ef2c0fcd448e32b0544a7ac2d906c5e599ed2fa555dcb10 computed Draft Figure 2 PNG. figure_2 v0.1.0-20260706 results/nar_figures/figure3_benchmark_model_comparison.svg yes figure public_ready 37644 7b276104d5f05e8f5ba954706d0d426bdc05ea356e9c0580d0320d4d26eab11e computed Draft Figure 3 SVG: benchmark and model-comparison ladder. figure_3 v0.1.0-20260706 results/nar_figures/figure3_benchmark_model_comparison.png yes figure public_ready 267189 0432d30943f86f74ae936454db854aecb9ec55cc5226e5114a973380e3626e67 computed Draft Figure 3 PNG. 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7a8b86522193803eee6adcda33f179c39219db6b5b607ae904dbe38cd81a9c1c computed 16 Release category counts used in Figure 6. figure_6;supplementary_data v0.1.0-20260706 results/nar_figures/figure6_resource_schema_metrics.tsv yes figure_source_data public_ready 235 a9d34c6a60465b1e441b816cd9e5cb8dc21217fbb0ef12ec0798b21c1be2847e computed 10 Resource schema and portal metrics used in Figure 6. figure_6;supplementary_data v0.1.0-20260706 results/nar_figures/NAR_FIGURES_1_TO_6_OVERVIEW_CROPPED.png yes figure public_ready 1237593 ebc893fc1feda1f93f2f270228f5c6d8a918c9a90a7cfc37b238881df7b724a5 computed Overview PNG of current Figures 1-6 for manuscript inspection. figures;quality_control v0.1.0-20260706 results/nar_figures/NAR_FIGURE_SCAFFOLD_REPORT.md yes figure public_ready 1471 1fc33cc29b8ccd745112d6da9c6bdc902fd03e99c44f20e5062aa9200bc79b51 computed Figure scaffold report. figures;methods v0.1.0-20260706 manuscript/NMD_VCELL_NAR_MANUSCRIPT_SCAFFOLD.md yes manuscript public_ready 6761 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