{
  "schemaVersion": 1,
  "analysis": {
    "id": "gse65145",
    "title": "Rapamycin in human fibroblasts: BUB1B locus RNA signal",
    "group": "reanalysis"
  },
  "generatedAt": "2026-10-25T05:00:13.621Z",
  "generatedBy": "BioLab Analysis Tools (www.stackfire.com)",
  "dates": {
    "archivedRecordedOn": "2026-10-10",
    "snapshotDataAsOf": "2026-10-17",
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      },
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        "executedAt": "2026-10-24T20:35:58.556365+00:00",
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      {
        "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": "gillespie-2015",
      "title": "Gillespie et al. — rapamycin and normal human fibroblast transcription",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4915505/",
      "doi": "10.1080/19491034.2015.1128610",
      "pmid": "26652669"
    }
  ],
  "model": "One normal human 2DD foreskin fibroblast line; no MVA genotype, no BUBR1 protein measurement.",
  "samples": "Six samples: two proliferative vehicle (10% FBS, DMSO), two reduced serum (0.5% FBS, five days), two rapamycin (500 nM, five days, 10% FBS). Two biological samples per condition.",
  "parameters": [
    "Anchor: NM_001211.6 (BUB1B) span on hg19",
    "Feature selection: at least 99% reciprocal overlap with the anchor, then minimum boundary distance",
    "Estimator: arithmetic means of RPKM as deposited; ratios of means per condition"
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      "url": "https://api.genome.ucsc.edu/getData/track?genome=hg19;track=ncbiRefSeq;chrom=chr15;start=40000000;end=41000000",
      "reason": "Archived public annotation input. Live response includes changing download timestamp; preserve source bytes, not a regenerated analysis output.",
      "bundled": true
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  ],
  "script": {
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    "sha256": "a66f9c10b93031ec620e812de59e717d35272657fdd0d56d6ea7c11230df807a",
    "url": "https://github.com/ivillafuerte/mva-hackathon-2026/blob/a434af99342f57aa9fde958535c173b82c315c2a/track2/reproduction/gse65145/reanalyse_gse65145.py"
  },
  "command": "python reanalyse_gse65145.py",
  "archived": {
    "snapshotId": "mva-results-2026-10-17-immunotherapy-audit-v1",
    "recordId": "MVA-RAP-GSE65145-001",
    "provenance": {
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      "method": "Parse six deposited hg19 RPKM tracks; require >=99% reciprocal overlap with RefSeq NM_001211.6; select minimum boundary-distance feature and calculate ratios of arithmetic means. Check all three qualifying features.",
      "verification": "All six coordinate arrays match; each has 149122 rows. Eighteen rows overlap the anchor and three qualify. GEO sample titles and artifact hashes verified. Complete reproducible package saved separately; no human scientific review or new biological experiment is claimed."
    }
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      "inputs": {
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      "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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          "numpy": "2.3.5",
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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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      "executedAt": "2026-10-24T20:35:58.556365+00:00",
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      "inputs": {
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    {
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      },
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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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  ],
  "values": [
    {
      "key": "rows",
      "label": "Rows per processed track",
      "value": "149,122",
      "unit": "rows",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.gse65145.gse65145_bub1b_results.json"
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      "unit": "rows",
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    },
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      "value": "3",
      "unit": "features",
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        "fileId": "stackfire-20261024-python312.gse65145.gse65145_bub1b_results.json"
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    },
    {
      "key": "span",
      "label": "Primary feature span",
      "value": "chr15:40453238–40513321",
      "unit": "hg19, 0-based start",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.gse65145.gse65145_bub1b_results.json"
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    },
    {
      "key": "meanPro",
      "label": "Mean RPKM, proliferative vehicle",
      "value": "5.898982",
      "unit": "RPKM as deposited",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
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    },
    {
      "key": "meanQui",
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      "unit": "RPKM as deposited",
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    },
    {
      "key": "meanRap",
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      "unit": "RPKM as deposited",
      "source": {
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    },
    {
      "key": "rapPro",
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    },
    {
      "key": "quiPro",
      "label": "Qui / Pro ratio of means",
      "value": "0.186191",
      "unit": "ratio",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
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    },
    {
      "key": "rapQui",
      "label": "Rap / Qui ratio of means",
      "value": "3.145731",
      "unit": "ratio",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.gse65145.gse65145_bub1b_results.json"
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    },
    {
      "key": "percent",
      "label": "Rapamycin versus proliferative, primary feature",
      "value": "−41.43",
      "unit": "%",
      "source": {
        "label": "gse65145_bub1b_results.json (stackfire-20261024-python312)",
        "fileId": "stackfire-20261024-python312.gse65145.gse65145_bub1b_results.json"
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  "limitations": [
    "Unstranded genomic-span features, not direct BUBR1 protein measurements or validated mature transcript isoform estimates.",
    "Three overlapping features are sensitivity views of the same locus, not independent biological replicates.",
    "Two biological replicates per condition from one normal cell line; no MVA genotype and no donor-level replication.",
    "Serum reduction is a useful control but is not matched to rapamycin for cell-cycle distribution; no causal proliferation adjustment is claimed.",
    "Continuous 500 nM/five-day treatment; no washout, transient exposure, aneuploidy, mitotic checkpoint or rescue endpoint.",
    "Published normalized RPKM values are used as deposited without re-alignment, count-based differential expression, an added pseudocount, p-values or rescue probabilities.",
    "149122 rows were observed in each deposited track; the paper states 149135 probes. The 13-row difference is not resolved here.",
    "This does not establish that BUBR1 protein falls, rule out post-transcriptional effects, or predict clinical harm or benefit."
  ],
  "whatItIsNot": "An RNA feature in normal fibroblasts, not BUBR1 protein, not an MVA model and not a rescue. Reduced serum is not a cell-cycle-matched control; proliferation confounding is unresolved."
}