{
  "schemaVersion": 1,
  "analysis": {
    "id": "ptc",
    "title": "L737* readthrough: exact versus nearby contexts",
    "group": "reanalysis"
  },
  "generatedAt": "2026-10-25T04:59:27.334Z",
  "generatedBy": "BioLab Analysis Tools (www.stackfire.com)",
  "dates": {
    "archivedRecordedOn": "2026-10-09",
    "snapshotDataAsOf": "2026-10-17",
    "executions": [
      {
        "id": "stackfire-20261024-python313",
        "origin": "stackfire",
        "executedAt": null,
        "recordedAt": "2026-10-24T23:32:43.816Z",
        "executionTimeSource": null,
        "timingNote": "The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown."
      },
      {
        "id": "stackfire-20261024-python312",
        "origin": "stackfire",
        "executedAt": null,
        "recordedAt": "2026-10-24T23:32:43.620Z",
        "executionTimeSource": null,
        "timingNote": "The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown."
      },
      {
        "id": "replay-check-20261024",
        "origin": "repository",
        "executedAt": "2026-10-24T20:35:58.556365+00:00",
        "recordedAt": null,
        "executionTimeSource": null,
        "timingNote": null
      },
      {
        "id": "execution-check-20261022",
        "origin": "repository",
        "executedAt": "2026-10-22T18:59:19.720827+00:00",
        "recordedAt": null,
        "executionTimeSource": null,
        "timingNote": null
      }
    ],
    "note": "generatedAt is the moment this manifest was written; it is not an execution or publication date. recordedAt is packaging time; a null executedAt means the actual execution time is unknown."
  },
  "repository": {
    "sha": "a434af99342f57aa9fde958535c173b82c315c2a",
    "short": "a434af9",
    "repository": "https://github.com/ivillafuerte/mva-hackathon-2026",
    "treeUrl": "https://github.com/ivillafuerte/mva-hackathon-2026/tree/a434af99342f57aa9fde958535c173b82c315c2a"
  },
  "sources": [
    {
      "id": "toledano-2024",
      "title": "Toledano et al. — genome-scale PTC readthrough",
      "url": "https://www.nature.com/articles/s41588-024-01878-5",
      "doi": "10.1038/s41588-024-01878-5",
      "pmid": "39174735"
    },
    {
      "id": "omachi-2022",
      "title": "Omachi et al. — COL4A5 readthrough reporters",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8866893/",
      "doi": "10.1016/j.isci.2022.103891",
      "pmid": "35243249"
    }
  ],
  "model": "Published 144-nt PTC reporters in HEK293T landing-pad cells; nearest six-base contexts, not endogenous BUB1B.",
  "samples": "Measured reporter rows nearest to the L737* six-base context (UGA, gagagt); untreated and gentamicin columns.",
  "parameters": [
    "Target context: gagagt (UGA)",
    "Selection: minimum six-base Hamming distance, without using response values",
    "Summaries: medians per treatment and median of within-row paired differences, in percentage points"
  ],
  "inputs": [
    {
      "path": "ptc/supp_tables.xlsx",
      "url": "https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41588-024-01878-5/MediaObjects/41588_2024_1878_MOESM4_ESM.xlsx",
      "sha256": "83b4661d839e7450abb3a4266a0dc7e94260fd100f9a6efcc6e2bd77683a5b64",
      "bytes": 10227370
    },
    {
      "path": "ptc/prediction_extracts.tsv",
      "sha256": "5db3ac1925af814552fad15153299e2dbafee484c00680a5369f7d7613a5ab5f",
      "url": "https://doi.org/10.6084/m9.figshare.23708901",
      "version_observed": 2,
      "reason": "Archived exact-coordinate extract; not freshly re-extracted in this reproduction.",
      "bundled": true
    }
  ],
  "script": {
    "path": "track2/reproduction/ptc/analyze.py",
    "sha256": "9b6e1085155fa229fa2816b56f4994541ce827008109b27f93cba33ca5c767a8",
    "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/ptc/analyze.py"
  },
  "command": "python analyze.py --workbook supp_tables.xlsx --predictions prediction_extracts.tsv --outdir results; python test_analysis.py",
  "archived": {
    "snapshotId": "mva-results-2026-10-17-immunotherapy-audit-v1",
    "recordId": "MVA-RT-002",
    "provenance": {
      "artifact": "l737_readthrough_gate_2026-10-09/results/results.json",
      "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
      "method": "Extracted medians from the existing nearest-context reanalysis. The paired median increment is not the difference of group medians.",
      "verification": "Imported an existing analysis artifact and computed its SHA-256. This snapshot build does not rerun the original analysis or validate biological efficacy."
    }
  },
  "executions": [
    {
      "id": "stackfire-20261024-python313",
      "origin": "stackfire",
      "executedAt": null,
      "recordedAt": "2026-10-24T23:32:43.816Z",
      "executionTimeSource": null,
      "timingNote": "The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown.",
      "environment": {
        "python": "3.13.17",
        "dependencies": {
          "pandas": "2.2.3",
          "numpy": "2.3.5",
          "scipy": "1.17.0",
          "openpyxl": "3.1.5"
        },
        "isolated": true,
        "pinned": false
      },
      "inputs": {
        "method": "Inputs fetched from the public URLs of input_manifest.json over the network, plus the two bundled public references; every byte count and SHA-256 compared with the manifest.",
        "verified": 14,
        "expected": 14
      },
      "artifacts": [
        {
          "analysis": "gse65145",
          "artifact": "gse65145/gse65145_bub1b_results.json",
          "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "expectedSha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "nmd",
          "artifact": "nmd/results/selected_candidates.csv",
          "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "expectedSha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "ptc",
          "artifact": "ptc/results/results.json",
          "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "expectedSha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "checkpoint",
          "artifact": "checkpoint/results.json",
          "sha256": "81d3ccfd003926d90b70928407c3e91c8f52d046e655ecdead644994240539e0",
          "expectedSha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "outputVerified": true,
          "matches": false,
          "normalisation": {
            "field": "software.python",
            "from": "3.13.17",
            "to": "3.12.14",
            "sha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
            "matchesArchived": true
          }
        }
      ],
      "note": "Same fresh inputs, CPython 3.13.17 in a new virtual environment: interpreter deliberately outside the pinned version to show which artifact depends on it."
    },
    {
      "id": "stackfire-20261024-python312",
      "origin": "stackfire",
      "executedAt": null,
      "recordedAt": "2026-10-24T23:32:43.620Z",
      "executionTimeSource": null,
      "timingNote": "The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown.",
      "environment": {
        "python": "3.12.3",
        "dependencies": {
          "pandas": "2.2.3",
          "numpy": "2.3.5",
          "scipy": "1.17.0",
          "openpyxl": "3.1.5"
        },
        "isolated": true,
        "pinned": false
      },
      "inputs": {
        "method": "Inputs fetched from the public URLs of input_manifest.json over the network, plus the two bundled public references; every byte count and SHA-256 compared with the manifest.",
        "verified": 14,
        "expected": 14
      },
      "artifacts": [
        {
          "analysis": "gse65145",
          "artifact": "gse65145/gse65145_bub1b_results.json",
          "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "expectedSha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "nmd",
          "artifact": "nmd/results/selected_candidates.csv",
          "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "expectedSha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "ptc",
          "artifact": "ptc/results/results.json",
          "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "expectedSha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "outputVerified": true,
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "checkpoint",
          "artifact": "checkpoint/results.json",
          "sha256": "c464fed27412ae21bcaf8925de98b04fbad70d758474320c5a977981312e502b",
          "expectedSha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "outputVerified": true,
          "matches": false,
          "normalisation": {
            "field": "software.python",
            "from": "3.12.3",
            "to": "3.12.14",
            "sha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
            "matchesArchived": true
          }
        }
      ],
      "note": "Fresh network downloads of all 12 public inputs on 2026-10-24, each verified against input_manifest.json; system CPython 3.12.3 in a new virtual environment (the pinned 3.12.14 build was not available on this host)."
    },
    {
      "id": "replay-check-20261024",
      "origin": "repository",
      "executedAt": "2026-10-24T20:35:58.556365+00:00",
      "recordedAt": null,
      "executionTimeSource": null,
      "timingNote": null,
      "environment": {
        "python": "3.12.14",
        "dependencies": {
          "pandas": "2.2.3",
          "numpy": "2.3.5",
          "scipy": "1.17.0",
          "openpyxl": "3.1.5"
        },
        "isolated": false,
        "pinned": true
      },
      "inputs": {
        "method": "Previously downloaded public cached bytes, each verified against the unchanged manifest; not a fresh network download.",
        "verified": 14,
        "expected": 14
      },
      "artifacts": [
        {
          "analysis": "gse65145",
          "artifact": "gse65145/gse65145_bub1b_results.json",
          "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "expectedSha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "nmd",
          "artifact": "nmd/results/selected_candidates.csv",
          "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "expectedSha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "ptc",
          "artifact": "ptc/results/results.json",
          "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "expectedSha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "checkpoint",
          "artifact": "checkpoint/results.json",
          "sha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "expectedSha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "matches": true,
          "normalisation": null
        }
      ],
      "note": "Run in the existing, non-isolated Python 3.12.14 environment before the sensitivity audit."
    },
    {
      "id": "execution-check-20261022",
      "origin": "repository",
      "executedAt": "2026-10-22T18:59:19.720827+00:00",
      "recordedAt": null,
      "executionTimeSource": null,
      "timingNote": null,
      "environment": {
        "python": "3.12.14",
        "dependencies": {
          "pandas": "2.2.3",
          "numpy": "2.3.5",
          "scipy": "1.17.0",
          "openpyxl": "3.1.5"
        },
        "isolated": true,
        "pinned": true
      },
      "inputs": {
        "method": "All 12 remote inputs fetched sequentially into a brand-new isolated virtual environment and verified against input_manifest.json.",
        "verified": 12,
        "expected": 12
      },
      "artifacts": [
        {
          "analysis": "gse65145",
          "artifact": "gse65145/gse65145_bub1b_results.json",
          "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "expectedSha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "nmd",
          "artifact": "nmd/results/selected_candidates.csv",
          "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "expectedSha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "ptc",
          "artifact": "ptc/results/results.json",
          "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "expectedSha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "matches": true,
          "normalisation": null
        },
        {
          "analysis": "checkpoint",
          "artifact": "checkpoint/results.json",
          "sha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "expectedSha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "matches": true,
          "normalisation": null
        }
      ],
      "note": "Recorded in the research repository. Successful computational reproduction under the stated input boundaries, not biological validation."
    }
  ],
  "values": [
    {
      "key": "exact",
      "label": "Exact six-base context matches",
      "value": "0",
      "unit": "rows",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "hamming",
      "label": "Nearest measured context, Hamming distance",
      "value": "1",
      "unit": "bases",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "rows",
      "label": "Nearest measured variant rows",
      "value": "12",
      "unit": "rows",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "untreatedMedian",
      "label": "Median readthrough, untreated",
      "value": "0.1745",
      "unit": "%",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "gentamicinMedian",
      "label": "Median readthrough, gentamicin",
      "value": "0.1985",
      "unit": "%",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "pairedMedian",
      "label": "Median paired increment (gentamicin − untreated)",
      "value": "+0.0165",
      "unit": "percentage points",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "l737",
      "label": "L737* present in the measured table",
      "value": "No",
      "unit": "boolean",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "bub1bRows",
      "label": "BUB1B variants present in the measured table",
      "value": "BUB1B_R114X",
      "unit": "list",
      "source": {
        "label": "results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.results.json"
      }
    },
    {
      "key": "contexts",
      "label": "Distinct six-base contexts among the nearest rows",
      "value": "8",
      "unit": "contexts",
      "source": {
        "label": "nearest_contexts.csv (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.ptc.results.nearest_contexts.csv"
      }
    }
  ],
  "crossChecks": [
    {
      "label": "Untreated median, chart versus results.json",
      "archived": 0.1745,
      "executed": 0.1745,
      "tolerance": 0,
      "agrees": true
    },
    {
      "label": "Gentamicin median, chart versus results.json",
      "archived": 0.1985,
      "executed": 0.1985,
      "tolerance": 0,
      "agrees": true
    },
    {
      "label": "Median paired increment quoted in the snapshot (0.0165) versus results.json",
      "archived": 0.0165,
      "executed": 0.016500000000000015,
      "tolerance": 0.00005,
      "agrees": true
    },
    {
      "label": "Nearest measured rows (12) versus results.json",
      "archived": 12,
      "executed": 12,
      "tolerance": 0,
      "agrees": true
    },
    {
      "label": "Distinct contexts (8, October 24 correction) versus nearest_contexts.csv",
      "archived": 8,
      "executed": 8,
      "tolerance": 0,
      "agrees": true
    }
  ],
  "files": [
    {
      "id": "script-ptc",
      "path": "track2/reproduction/ptc/analyze.py",
      "sha256": "9b6e1085155fa229fa2816b56f4994541ce827008109b27f93cba33ca5c767a8",
      "bytes": 6537,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/ptc/analyze.py",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/script-ptc"
    },
    {
      "id": "script-ptc-test",
      "path": "track2/reproduction/ptc/test_analysis.py",
      "sha256": "ac47c819e5b139d343929f67e62bf79b059ec4b1482fc94a33fb141747813b20",
      "bytes": 771,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/ptc/test_analysis.py",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/script-ptc-test"
    },
    {
      "id": "ptc-prediction-extract",
      "path": "track2/reproduction/ptc/prediction_extracts.tsv",
      "sha256": "5db3ac1925af814552fad15153299e2dbafee484c00680a5369f7d7613a5ab5f",
      "bytes": 663,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/ptc/prediction_extracts.tsv",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/ptc-prediction-extract"
    },
    {
      "id": "input-manifest",
      "path": "track2/reproduction/input_manifest.json",
      "sha256": "71839d51558a1ff86c5c9c15ce6948f3a45e32eedd4e8b36f9e02ab7cc26bd46",
      "bytes": 4123,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/input_manifest.json",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/input-manifest"
    },
    {
      "id": "original-script-hashes",
      "path": "track2/reproduction/original_script_hashes.json",
      "sha256": "f1cf273298d00d7d7c92be82beb691c0e59e0186a3459a019c8752ff631c925f",
      "bytes": 476,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/original_script_hashes.json",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/original-script-hashes"
    },
    {
      "id": "requirements",
      "path": "track2/reproduction/requirements.txt",
      "sha256": "864ff6d6156a3101bdcb73aba6c3565763143808c81f408f0b8c2214c62c9080",
      "bytes": 57,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/requirements.txt",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/requirements"
    },
    {
      "id": "fetch-inputs",
      "path": "track2/reproduction/fetch_inputs.py",
      "sha256": "b12696b6387d5120d1ab49528576e7b90153cf098c29ecc06babb46797a30d99",
      "bytes": 1478,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/fetch_inputs.py",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/fetch-inputs"
    },
    {
      "id": "run-reanalyses",
      "path": "track2/reproduction/run_reanalyses.py",
      "sha256": "3ccbd544b2c119b0c2558ea4ea172bf37c4a100e569fe047b2f16d95274713ea",
      "bytes": 3460,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/run_reanalyses.py",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/run-reanalyses"
    },
    {
      "id": "stackfire-20261024-python313.execution.json",
      "path": "executions/stackfire-20261024-python313/execution.json",
      "sha256": "3e96a613c786bd72e045f0678e9f063aa551ab0821296efe28e84cc2432d3ff9",
      "bytes": 12164,
      "url": null,
      "href": "http://www.stackfire.com/api/biolab/analysis/files/stackfire-20261024-python313.execution.json"
    },
    {
      "id": "stackfire-20261024-python312.execution.json",
      "path": "executions/stackfire-20261024-python312/execution.json",
      "sha256": "1356584c9c89ff15209c9af82ba5b4e1385545f7e351dcd3763772de5b73a5b7",
      "bytes": 12223,
      "url": null,
      "href": "http://www.stackfire.com/api/biolab/analysis/files/stackfire-20261024-python312.execution.json"
    },
    {
      "id": "replay-check-20261024",
      "path": "track2/reproduction/robustness/verification/deterministic_replay_check_20261024.json",
      "sha256": "c6eb2ccde8c0fb3f297ecf715a2d1808a78a2eb6fdab5f3d7eeba0625527894a",
      "bytes": 1750,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/robustness/verification/deterministic_replay_check_20261024.json",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/replay-check-20261024"
    },
    {
      "id": "execution-check-20261022",
      "path": "track2/reproduction/execution_check.json",
      "sha256": "38ed7fccba9f110ac6a832a950f42a6c001d07666ec134a0e5e2f189653fbe55",
      "bytes": 1749,
      "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/execution_check.json",
      "href": "http://www.stackfire.com/api/biolab/analysis/files/execution-check-20261022"
    }
  ],
  "limitations": [
    "Neighboring-context values are not a prediction for L737* or the child.",
    "The main predictive analysis excluded gentamicin for weak signal.",
    "Readthrough does not guarantee native leucine, endogenous transcript survival, or functional BUBR1. Gentamicin plus mefloquine remains an experimental branch only."
  ],
  "whatItIsNot": "There is no exact L737* measurement and no exact six-base match. Twelve measured rows represent eight distinct contexts; they are not BUB1B efficacy, not a patient prediction and not a rescue probability."
}