{
  "schemaVersion": 1,
  "analysis": {
    "id": "nmd",
    "title": "704-drug NMD screen: reporter specificity",
    "group": "reanalysis"
  },
  "generatedAt": "2026-10-25T04:59:44.444Z",
  "generatedBy": "BioLab Analysis Tools (www.stackfire.com)",
  "dates": {
    "archivedRecordedOn": "2026-10-09",
    "snapshotDataAsOf": "2026-10-17",
    "executions": [
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        "id": "stackfire-20261024-python313",
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        "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",
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      }
    ],
    "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": "zhao-2021",
      "title": "Zhao et al. — molecular profiling of NMD modulators",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8718828/",
      "doi": "10.1016/j.omtn.2021.12.003",
      "pmid": "35024243"
    }
  ],
  "model": "Published mouse Neuro-2a AS-NMD isoform summaries; three endogenous reporter genes (Ptbp2, Hnrnpl, Tra2b), not BUB1B.",
  "samples": "704 drugs plus one control at 5 µM for 5 h; summarised ratios without individual Ct replicates.",
  "parameters": [
    "Three NMD / non-NMD isoform ratios per drug",
    "Screen-wide Z and Fisher combination recomputed; Benjamini–Hochberg recomputed",
    "Published permutation q values reused, not rerun"
  ],
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      "sha256": "f7107fa8e401cc6d1d2adbb68adca5baefe63472cfaf2f178e667d678c3b0007",
      "bytes": 497402
    },
    {
      "path": "nmd/inputs/table_S4.xlsx",
      "url": "https://ars.els-cdn.com/content/image/1-s2.0-S2162253121003061-mmc5.xlsx",
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    "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/nmd/reanalyze.py"
  },
  "command": "python reanalyze.py",
  "archived": {
    "snapshotId": "mva-results-2026-10-17-immunotherapy-audit-v1",
    "recordId": "MVA-NMD-003",
    "provenance": {
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      "sha256": "ad7fa784e6caf2f126c9730e4edaf7dc75f0ea2ad54208661de75555ede6ab9c",
      "method": "Extracted named compounds and ratios from the existing independently reconstructed Table S2/S4 analysis; published q values are not clinical probabilities.",
      "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": [
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      "origin": "stackfire",
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      "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.",
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        "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": [
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        },
        {
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          "sha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "expectedSha256": "8d1f7ca32b05f9e85cedc5d025ea04efee60b581ae4effea8fd389e6f4afbcb9",
          "outputVerified": true,
          "matches": true,
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        },
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          "artifact": "checkpoint/results.json",
          "sha256": "81d3ccfd003926d90b70928407c3e91c8f52d046e655ecdead644994240539e0",
          "expectedSha256": "d6be3833115ac368fffe185dfea0e42439e4c80e723b88c626ecb9b874073e6c",
          "outputVerified": true,
          "matches": false,
          "normalisation": {
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            "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": {
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        "dependencies": {
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          "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": [
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          "sha256": "e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6",
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          "matches": true,
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      ],
      "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": {
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        "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": [
        {
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      "note": "Run in the existing, non-isolated Python 3.12.14 environment before the sensitivity audit."
    },
    {
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        "pinned": true
      },
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      "note": "Recorded in the research repository. Successful computational reproduction under the stated input boundaries, not biological validation."
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  "limitations": [
    "Normalized RNA ratios cannot isolate decay from splicing or isoform regulation.",
    "Replicate Ct values are unavailable. Published ratio SEM formulas do not provide valid replicate-based uncertainty; no error bars are shown.",
    "Translation inhibition is counterevidence for homoharringtonine. Statistical significance is not therapeutic suitability."
  ],
  "whatItIsNot": "A reporter screen in mouse cells. No BUB1B was measured; statistical significance is not therapeutic suitability and no hit establishes functional BUBR1 rescue."
}