{
  "checker": {
    "claims": [
      {
        "claim": "Create an isolated modelling session",
        "command": "<guest-path> tools/call {\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass probe\"}}",
        "evidence": "\u2026Created session: 78f3b230-5bf9-4f84-958e-3facd8191b72 (coldpass probe)\", \"type\": \"text\"}], \"isError\": false, \"structuredContent\": {\"result\": \"Created session: 78f3b230-5bf9-4f84-958e-3facd8191b72 (coldpass probe)\"}}",
        "expected": "Created session:",
        "input": "{\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass probe\"}}",
        "kind": "claim",
        "outcome": "Real input produced the expected result: Created session:",
        "source": "Each server can maintain multiple isolated modelling sessions.",
        "source_checked": true,
        "source_file": "README.md",
        "verdict": "yes"
      }
    ],
    "cycle_checks": [
      {
        "claim": "Scheduled or looping main behavior",
        "command": "",
        "evidence": "Inspected the root README and NeKo README workflows; no scheduled job, recurring loop, webhook trigger, or one-shot cycle entrypoint is documented.",
        "expected": "identify the product trigger",
        "input": "source inspection",
        "kind": "cycle",
        "outcome": "Inspected the root README and NeKo README workflows; no scheduled job, recurring loop, webhook trigger, or one-shot cycle entrypoint is documented.",
        "source": "repository entry points",
        "verdict": "yes"
      }
    ],
    "details": {
      "argv": [
        "<guest-path>"
      ],
      "kind": "mcp",
      "scope": "product operation",
      "serverInfo": {
        "description": "Build and analyze signalling networks from biological interaction databases.",
        "name": "NeKo",
        "title": "NeKo Signalling Network Builder",
        "version": "2.5.2"
      },
      "tool_result": {
        "content": [
          {
            "text": "Created session: c135f2bb-b749-428e-8fd5-6577ac55df94 (coldpass probe)",
            "type": "text"
          }
        ],
        "isError": false,
        "structuredContent": {
          "result": "Created session: c135f2bb-b749-428e-8fd5-6577ac55df94 (coldpass probe)"
        }
      },
      "tool_result_checked": true,
      "tool_schema_bytes": 93149,
      "tools": [
        "analyze_gene_set",
        "analyze_connectivity",
        "edit_interactions",
        "export_handoff_bundle",
        "list_network_history",
        "navigate_network_history",
        "compare_network_states",
        "set_network_history_limit",
        "create_network",
        "add_nodes",
        "remove_gene",
        "remove_interaction",
        "export_network",
        "export_neko_handoff",
        "list_genes_and_interactions",
        "find_paths",
        "reset_network",
        "clean_generated_files",
        "remove_bimodal_interactions",
        "remove_undefined_interactions",
        "list_bnet_files",
        "get_references",
        "set_default_params",
        "filter_interactions",
        "create_session",
        "list_sessions",
        "list_artifact_sessions",
        "set_default_session",
        "delete_session",
        "status",
        "preview_connection_impact",
        "bridge_components",
        "connect_targeted_nodes",
        "apply_global_connection",
        "export_biomass_handoff"
      ],
      "working": true
    },
    "evidence_strength": "readme_checked",
    "example_checks": [
      {
        "claim": "Start the installed NeKo MCP server",
        "command": "<guest-path>",
        "deferred": false,
        "evidence": "",
        "expected": "Created session:",
        "input": "stdio MCP session",
        "kind": "example",
        "outcome": "command completed successfully with no output",
        "returncode": 0,
        "source": "NeKo/README.md \u2014 Installation and startup",
        "verdict": "yes"
      }
    ],
    "status": "PASS"
  },
  "deviations": [
    "Initial global install command `python3 -m pip install mcp-biomodelling-servers` failed: externally-managed-environment; retried successfully inside virtualenv.",
    "First MCP start reported missing libXrender.so.1; installed libxrender1 and retried successfully."
  ],
  "fault_owner": null,
  "main_blocker": null,
  "operation": "Start the NeKo stdio MCP server and create an isolated modelling session",
  "operation_scope": "Python 3.12.3; mcp-biomodelling-servers 2.5.2 and declared modelling dependencies installed in <guest-path>",
  "outcome": "working",
  "plain_failure": null,
  "steps": [
    "Read README requirements and NeKo installation/workflow guide",
    "Created a Python 3.12 virtual environment after global pip installation was rejected by PEP 668",
    "Installed mcp-biomodelling-servers and declared dependencies",
    "Installed missing Ubuntu runtime library libxrender1 after PyGraphviz raised ImportError",
    "Started NeKo via its installed console entrypoint and called create_session",
    "Validated and replayed probe, README claim, example, and cycle assessment successfully"
  ],
  "stuck_step": null,
  "suggested_fix": null
}