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{
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          "mcp_bioconductor-clustifyr",
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          "mcp_bioconductor-curatedatlasqueryr",
          "mcp_bioconductor-cytomapper",
          "mcp_bioconductor-dada2",
          "mcp_bioconductor-data-packages",
          "mcp_bioconductor-decipher",
          "mcp_bioconductor-decontam",
          "mcp_bioconductor-decontx",
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          "mcp_bioconductor-delayedmatrixstats",
          "mcp_bioconductor-despace",
          "mcp_bioconductor-diffbind",
          "mcp_bioconductor-dino",
          "mcp_bioconductor-dirichletmultinomial",
          "mcp_bioconductor-dnacopy",
          "mcp_bioconductor-dose",
          "mcp_bioconductor-ensembldb",
          "mcp_bioconductor-erma",
          "mcp_bioconductor-escher",
          "mcp_bioconductor-experimentsubset",
          "mcp_bioconductor-fgsea",
          "mcp_bioconductor-genefilter",
          "mcp_bioconductor-geneplotter",
          "mcp_bioconductor-genomeinfodb",
          "mcp_bioconductor-genomeinfodbdata",
          "mcp_bioconductor-genomicalignments",
          "mcp_bioconductor-genomicfeatures",
          "mcp_bioconductor-genomicranges",
          "mcp_bioconductor-geomxtools",
          "mcp_bioconductor-ggsc",
          "mcp_bioconductor-ggspavis",
          "mcp_bioconductor-ggtree",
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          "mcp_bioconductor-go.db",
          "mcp_bioconductor-gosemsim",
          "mcp_bioconductor-graph",
          "mcp_bioconductor-gsva",
          "mcp_bioconductor-hcatonsildata",
          "mcp_bioconductor-hdf5array",
          "mcp_bioconductor-hoodscanr",
          "mcp_bioconductor-humanhippocampus2024",
          "mcp_bioconductor-imcdatasets",
          "mcp_bioconductor-imcrtools",
          "mcp_bioconductor-impute",
          "mcp_bioconductor-infercnv",
          "mcp_bioconductor-interactivedisplaybase",
          "mcp_bioconductor-iranges",
          "mcp_bioconductor-irisfgm",
          "mcp_bioconductor-jazzpanda",
          "mcp_bioconductor-keggrest",
          "mcp_bioconductor-lisaclust",
          "mcp_bioconductor-mastr",
          "mcp_bioconductor-matrixgenerics",
          "mcp_bioconductor-merfishdata",
          "mcp_bioconductor-metabolomicsworkbenchr",
          "mcp_bioconductor-metapod",
          "mcp_bioconductor-mia",
          "mcp_bioconductor-moleculeexperiment",
          "mcp_bioconductor-mosim",
          "mcp_bioconductor-mousegastrulationdata",
          "mcp_bioconductor-mspurity",
          "mcp_bioconductor-multiassayexperiment",
          "mcp_bioconductor-multtest",
          "mcp_bioconductor-nebulosa",
          "mcp_bioconductor-nnsvg",
          "mcp_bioconductor-noiseq",
          "mcp_bioconductor-orfhunter",
          "mcp_bioconductor-org.ce.eg.db",
          "mcp_bioconductor-org.hs.eg.db",
          "mcp_bioconductor-org.mm.eg.db",
          "mcp_bioconductor-partcnv",
          "mcp_bioconductor-phemd",
          "mcp_bioconductor-phyloseq",
          "mcp_bioconductor-pipecomp",
          "mcp_bioconductor-poem",
          "mcp_bioconductor-preprocesscore",
          "mcp_bioconductor-proteomicsannotationhubdata",
          "mcp_bioconductor-protgenerics",
          "mcp_bioconductor-qvalue",
          "mcp_bioconductor-rbgl",
          "mcp_bioconductor-reactomegsa.data",
          "mcp_bioconductor-regionalst",
          "mcp_bioconductor-rforproteomics",
          "mcp_bioconductor-rgraphviz",
          "mcp_bioconductor-rhdf5",
          "mcp_bioconductor-rhdf5filters",
          "mcp_bioconductor-rhdf5lib",
          "mcp_bioconductor-rhtslib",
          "mcp_bioconductor-rsamtools",
          "mcp_bioconductor-rsubread",
          "mcp_bioconductor-scaledmatrix",
          "mcp_bioconductor-scalign",
          "mcp_bioconductor-scarray.sat",
          "mcp_bioconductor-scbfa",
          "mcp_bioconductor-scbubbletree",
          "mcp_bioconductor-sccb2",
          "mcp_bioconductor-scclassifr",
          "mcp_bioconductor-scdataviz",
          "mcp_bioconductor-scdotplot",
          "mcp_bioconductor-scfeatures",
          "mcp_bioconductor-scider",
          "mcp_bioconductor-scmageck",
          "mcp_bioconductor-scqtltools",
          "mcp_bioconductor-scran",
          "mcp_bioconductor-screpertoire",
          "mcp_bioconductor-scrnaseq",
          "mcp_bioconductor-sctreeviz",
          "mcp_bioconductor-scuttle",
          "mcp_bioconductor-scvir",
          "mcp_bioconductor-seraster",
          "mcp_bioconductor-shortread",
          "mcp_bioconductor-signifinder",
          "mcp_bioconductor-singlecellmultimodal",
          "mcp_bioconductor-smoothclust",
          "mcp_bioconductor-smoppix",
          "mcp_bioconductor-sosta",
          "mcp_bioconductor-spacetrooper",
          "mcp_bioconductor-spaniel",
          "mcp_bioconductor-spari",
          "mcp_bioconductor-sparsematrixstats",
          "mcp_bioconductor-spatialcpie",
          "mcp_bioconductor-spatialdatasets",
          "mcp_bioconductor-spatialdecon",
          "mcp_bioconductor-spatialdmelxsim",
          "mcp_bioconductor-spatialexperiment",
          "mcp_bioconductor-spatialexperimentio",
          "mcp_bioconductor-spatialfda",
          "mcp_bioconductor-spatialfeatureexperiment",
          "mcp_bioconductor-spatialheatmap",
          "mcp_bioconductor-speckle",
          "mcp_bioconductor-spoon",
          "mcp_bioconductor-spotclean",
          "mcp_bioconductor-spotsweeper",
          "mcp_bioconductor-standr",
          "mcp_bioconductor-statial",
          "mcp_bioconductor-stjoincount",
          "mcp_bioconductor-summarizedexperiment",
          "mcp_bioconductor-svp",
          "mcp_bioconductor-tenxxeniumdata",
          "mcp_bioconductor-tidyomics",
          "mcp_bioconductor-tidyspatialexperiment",
          "mcp_bioconductor-treesummarizedexperiment",
          "mcp_bioconductor-tximport",
          "mcp_bioconductor-variantannotation",
          "mcp_bioconductor-vectrapolarisdata",
          "mcp_bioconductor-visiumio",
          "mcp_bioconductor-weberdivechalcdata",
          "mcp_bioconductor-xcms",
          "mcp_bioconductor-xenlite",
          "mcp_bioconductor-xvector",
          "mcp_bioconductor-zlibbioc",
          "mcp_biopython",
          "mcp_bowtie",
          "mcp_bowtie2",
          "mcp_bpipe",
          "mcp_brooklyn_plot",
          "mcp_busco",
          "mcp_bx-python",
          "mcp_c-ares",
          "mcp_cascade-reg",
          "mcp_cd-hit",
          "mcp_cdbtools",
          "mcp_cell2cell",
          "mcp_cellitac",
          "mcp_cellqc",
          "mcp_cellrank",
          "mcp_cellsnake",
          "mcp_celltypist",
          "mcp_celltypist-so",
          "mcp_checkatlas",
          "mcp_checkm-genome"
        ]
      }
    }
  },
  "aggregate": {
    "run_count": 2,
    "mean_retrieval_recall@1": 0.45,
    "mean_retrieval_recall@3": 0.7,
    "mean_retrieval_recall@5": 0.8,
    "mean_retrieval_recall@10": 0.8,
    "mean_retrieval_recall@20": 0.8,
    "mean_retrieval_recall@50": 0.8,
    "tool_selection_accuracy": 1.0,
    "workflow_validity": 1.0,
    "execution_success_rate": 1.0,
    "mean_context_tokens_rough": 1315.5,
    "mean_planning_latency_seconds": null
  },
  "results": [
    {
      "task_id": "evolution",
      "run_dir": "/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/evolution_20260513_070125",
      "retrieval_recall_at_k": {
        "1": 0.4,
        "3": 0.7,
        "5": 0.8,
        "10": 0.8,
        "20": 0.8,
        "50": 0.8
      },
      "tool_selection_accuracy": true,
      "workflow_validity": {
        "valid": true,
        "steps_matched": 4,
        "steps_total": 4,
        "matched_step_names": [
          "align_reads",
          "call_variants",
          "annotate_effects",
          "intersect_evolved_lines"
        ]
      },
      "execution_success": true,
      "context_tokens_rough": 1303,
      "planning_latency_seconds": null,
      "retrieved_candidate_count": 2911,
      "execution_evidence_count": 16560
    },
    {
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}