{
  "run_id": "marcorusc--mcp-biomodelling-servers-claude-haiku-5-5-1793176561604258445",
  "date": "2026-10-28T08:43:06.415758+00:00",
  "repo": "marcorusc/mcp-biomodelling-servers",
  "kind": "mcp",
  "source": "https://github.com/marcorusc/mcp-biomodelling-servers",
  "commit": "d9079ee2eb8965d27939631da98117abe774091b",
  "model": "claude-haiku-5-5",
  "model_version": "claude-haiku-5-5",
  "test_version": "readme-2d57868128a84902c09a58991c46c5fe288928e55b1de8282ab5003e13159c2f",
  "pass": true,
  "outcome": "pass",
  "time_to_working_s": 383.25467673699313,
  "total_s": 424.81138491630554,
  "steps": [
    "cd <guest-path> && pwd && ls -la && git status 2>&1 | head -3; python3 --version; cat README.md 2>/dev/null | head -c 6000",
    "curl -s -m 10 -i $CDP_URL/json/version; echo; echo \"exit=$?\"; echo \"CDP_URL=$CDP_URL\"; ls /inputs 2>&1",
    "cd <guest-path> && sed -n '/### Enabling/,/## /p' README.md | head -c 100 >/dev/null; grep -n '^#' README.md; ls .coldpass; ls <guest-path> 2>&1",
    "cd <guest-path> && sed -n '146,220p;258,300p' README.md",
    "python3 -m venv <guest-path> 2>&1 | tail -3; ls <guest-path> 2>&1 | head",
    "cd <guest-path> && timeout 900 <guest-path> -m pip install --upgrade pip ><guest-path> 2>&1; echo rc=$?; timeout 1500 <guest-path> -m pip install \"mcp-biomodelling-servers\" > <guest-path> 2>&1; echo rc=$?; tail -5 <guest-path>",
    "cd /tmp && for s in neko maboss physicell biomass; do <guest-path> --version; echo \"rc=$?\"; done; <guest-path> --help | head -30",
    "head -c 3000 <guest-path>; echo; grep -n \"def \\|argparse\" <guest-path> | head -60",
    "cd <guest-path> && ls MaBoSS mcp_biomodelling_servers; grep -rn \"@mcp.tool\\<email>\\|def create\\|def list_\" MaBoSS/*.py | head -40",
    "cd <guest-path> && sed -n 185,240p MaBoSS/server.py",
    "cd <guest-path> && grep -n \"All four servers use MCP over stdio\\|Each one serves MCP over stdio\\|Each server can maintain multiple\\|Prebuilt wheels cover\\|No system software is needed\\|python -m pip install mcp-biomodelling-servers\\|installs four console\\|The installation provides four console\" README.md",
    "cd <guest-path> && cat > probe.json <<'EOF'\n{\"kind\":\"mcp\",\"argv\":[\"<guest-path>\"],\"cwd\":\"<guest-path>\",\"tool\":\"create_session\",\"arguments\":{\"label\":\"coldpass-probe-7319\"},\"expected_text\":\"coldpass-probe-7319\"}\nEOF\ncat > claims.json <<'EOF'\n[{\"kind\":\"claim\",\"claim\":\"Each server can maintain multiple isolated modelling sessions; a MaBoSS session is created and its label is returned\",\"source\":\"Each server can maintain multiple isolated modelling sessions.\",\"input\":\"create_session with label coldpass-claim-5521\",\"expected\":\"session created with that label returned\",\"probe_kind\":\"mcp\",\"argv\":[\"<guest-path>\"],\"tool\":\"create_session\",\"arguments\":{\"label\":\"coldpass-claim-5521\"},\"expected_text\":\"coldpass-claim-5521\",\"cwd\":\"<guest-path>\"}]\nEOF\npython3 -m json.tool probe.json >/dev/null && python3 -m json.tool claims.json >/dev/null && echo ok",
    "cd <guest-path> && <env-var>=<guest-path> timeout 900 python3 -I <guest-path> --validate --replay 2>&1 | tail -c 5000; echo \"rc=${PIPESTATUS[0]}\"",
    "cd <guest-path> && grep -n -i \"pytest\\|test\\|cron\\|--once\\|--now\\|webhook\\|schedul\" README.md | head -20; ls tests | head -30; ls .github/workflows 2>/dev/null",
    "cd <guest-path> && cat > cycles.json <<'EOF'\n{\"detected\":false,\"checks\":[],\"reason\":\"Inspected README.md (Installation, Configure an MCP client, Sessions/artifacts, Run from source) and the four console entry points (mcp-neko-server, mcp-maboss-server, mcp-physicell-server, mcp-biomass-server). They serve MCP over stdio and expose no cron, loop, webhook, --once or --now trigger. The only CI schedule is in .github/workflows, which is not a product cycle.\"}\nEOF\ncat > examples.json <<'EOF'\n[]\nEOF\npython3 -m json.tool cycles.json >/dev/null && python3 -m json.tool examples.json >/dev/null && echo ok",
    "cd <guest-path> && <env-var>=<guest-path> timeout 900 python3 -I <guest-path> --validate --replay 2>&1 | head -c 1500; echo; echo \"rc=${PIPESTATUS[0]}\"",
    "cd <guest-path> && grep -n '^version\\|^name' pyproject.toml; timeout 1500 <guest-path> -m pip install --force-reinstall --no-deps \".\" > <guest-path> 2>&1; echo rc=$?; tail -2 <guest-path>; cd /tmp && <guest-path> --version",
    "cd <guest-path> && ls -d build *.egg-info 2>/dev/null; find . -name \"*.egg-info\" -maxdepth 2 | head; <env-var>=<guest-path> timeout 900 python3 -I <guest-path> --validate --replay 2>&1 | head -c 400; echo; echo \"rc=${PIPESTATUS[0]}\"",
    "cd <guest-path> && cat > report.json <<'EOF'\n{\"outcome\":\"working\",\"fault_owner\":null,\"operation\":\"Install mcp-biomodelling-servers from the source checkout and drive the MaBoSS MCP server over stdio: call create_session with a label and read the returned session ID and label.\",\"operation_scope\":\"Linux guest, Python 3.12.3 venv at <guest-path> (README requires Python 3.10-3.15). Covers the MaBoSS server only; NeKo, PhysiCell and BioMASS entry points were installed and report version 2.5.2 but were not exercised. No browser needed; CDP endpoint http://<internal-ip>:9226/json/version returned HTTP 200 (Chrome/155.0.8059.84) but no browser operation was run.\",\"steps\":[\"python3 -m venv <guest-path>\",\"<guest-path> -m pip install --upgrade pip\",\"<guest-path> -m pip install mcp-biomodelling-servers (initial install, then replaced)\",\"<guest-path> -m pip install --force-reinstall --no-deps . (run from <guest-path>, README 'Run from source')\",\"<guest-path> --version -> mcp-maboss-server (mcp-biomodelling-servers) 2.5.2\",\"MCP tools/call create_session {\\\"label\\\":\\\"coldpass-probe-7319\\\"} via <guest-path> -> 'Session created: <uuid> (coldpass-probe-7319) (set as default)'\",\"<env-var>=<guest-path> python3 -I <guest-path> --validate --replay -> valid true, replay PASS\"],\"deviations\":[\"Preflight path /inputs/coldpass-preflight.py does not exist in this VM; used <guest-path> as instructed by the checker path.\",\"First installed the PyPI release of 2.5.2, then reinstalled from the workspace source as README 'Run from source' describes; both report version 2.5.2 and the final replay used the source build.\",\"Workspace has no .git metadata; the pinned git fetch/reset was not performed because the source was already present and no git operation was needed to run the product. The pinned commit d9079ee2eb8965d27939631da98117abe774091b could not be verified in the guest.\",\"README documents no test command or example invocation beyond --help/--version, so examples.json is empty; the repo's offline pytest suite was not run as product evidence.\",\"Cycles: no cron, loop, webhook, --once or --now behavior in the product, so detected=false.\"],\"stuck_step\":null,\"main_blocker\":null,\"plain_failure\":null,\"suggested_fix\":\"None required for the exercised MaBoSS path. Optionally add a documented example command to the README so examples can be replayed.\"}\nEOF\npython3 -m json.tool report.json >/dev/null && echo ok; ls -la <guest-path>"
  ],
  "stuck_step": null,
  "error_excerpt": null,
  "what_it_did": "Install mcp-biomodelling-servers from the source checkout and drive the MaBoSS MCP server over stdio: call create_session with a label and read the returned session ID and label.",
  "suggested_fix": null,
  "tokens_in": 386691,
  "tokens_out": 8184,
  "cost_usd": 0.013667279999999999,
  "usage_complete": true,
  "checks": [
    {
      "check": "operation",
      "status": "PASS",
      "details": {
        "working": true,
        "argv": [
          "<guest-path>"
        ],
        "kind": "mcp",
        "serverInfo": {
          "description": "Configure, simulate, analyze, and visualize Boolean models with MaBoSS.",
          "name": "MaBoSS",
          "title": "MaBoSS Boolean Model Simulator",
          "version": "2.5.2"
        },
        "tools": [
          "edit_maboss_readouts",
          "export_handoff_bundle",
          "create_session",
          "list_sessions",
          "list_artifact_sessions",
          "set_default_session",
          "delete_session",
          "import_neko_handoff",
          "bnet_to_bnd_and_cfg",
          "build_simulation",
          "run_simulation",
          "export_maboss_bnd_cfg",
          "export_maboss_handoff",
          "get_maboss_nodes",
          "get_maboss_initial_state",
          "get_maboss_logical_rules",
          "change_maboss_rule",
          "get_maboss_mutations",
          "update_maboss_parameters",
          "set_maboss_output_nodes",
          "set_maboss_initial_state",
          "simulate_mutation",
          "visualize_network_trajectories",
          "get_simulation_result",
          "list_generated_files",
          "clean_generated_files"
        ],
        "tool_schema_bytes": 74564,
        "tool_result": {
          "content": [
            {
              "text": "Session created: 77e20301-ee04-46ac-9beb-e8030b8dfc77 (coldpass-probe-7319) (set as default)",
              "type": "text"
            }
          ],
          "isError": false,
          "structuredContent": {
            "result": "Session created: 77e20301-ee04-46ac-9beb-e8030b8dfc77 (coldpass-probe-7319) (set as default)"
          }
        },
        "tool_result_checked": true,
        "scope": "product operation"
      }
    }
  ],
  "safety": {
    "version": "z2x-1",
    "rules_version": "z2x-1",
    "summary": "No problems traced to this repository code in these checks.",
    "expected": "Reviewed as expected for a test run: attempted writes that failed, so nothing was written.",
    "findings": [],
    "context": [],
    "limitations": [
      "A short run cannot establish that code is safe.",
      "Connections show IP addresses; proxies can hide the final hostname.",
      "Tracing covers dispatched commands and their children, not the whole OS; guest root can interfere with tracing."
    ],
    "static": {
      "dependency_note": "OSV scanned supported lockfiles; unpinned dependencies and unsupported formats are outside this check."
    },
    "evidence_url": "/safety/?run=marcorusc--mcp-biomodelling-servers-claude-haiku-5-5-1793176561604258445",
    "evidence_file": "/data/safety/marcorusc--mcp-biomodelling-servers-claude-haiku-5-5-1793176561604258445.json.gz"
  },
  "agent_execution": "native_agent",
  "agent_runtime": "claude-code",
  "agent_runtime_version": "2.1.310 (Claude Code)",
  "tool_transport": "mcp-assigned-vm",
  "platform": "linux",
  "reasoning": "low",
  "service_tier": null,
  "resources": {
    "cpus": 2,
    "memory_mib": 4096,
    "disk_mib": 32768
  },
  "native_tool_calls": 19,
  "native_bundle": null,
  "architecture": null,
  "backend": "hyperv",
  "platform_details": {
    "backend": "hyperv",
    "os": "linux"
  },
  "platform_conflicts": null,
  "sandbox_source": null,
  "source_pin": {
    "commit": "d9079ee2eb8965d27939631da98117abe774091b",
    "url": "https://github.com/marcorusc/mcp-biomodelling-servers"
  },
  "purpose": "initial",
  "profile": {
    "model": "claude-haiku-5-5",
    "reasoning": "low"
  },
  "fault": {
    "owner": null,
    "status": "resolved",
    "reason": null
  },
  "fix_id": null,
  "verifies_run_id": null,
  "hosting": null,
  "operation_scope": "product operation",
  "tool_calls": 19,
  "guest_setup": null,
  "runtime": null,
  "runtime_version": null,
  "runtime_revision": null,
  "source_revision": null,
  "evidence_version": null,
  "failure_origin": null,
  "evidence_strength": "readme_checked",
  "works": "yes",
  "install_s": null,
  "first_use_s": null,
  "mcp": "local",
  "needs": [],
  "needs_which": null,
  "agent_interface": [
    "mcp"
  ],
  "license": "GPL-3.0",
  "repo_url": "https://github.com/marcorusc/mcp-biomodelling-servers",
  "cost_to_try": "free",
  "hardware": null,
  "what_failed": null,
  "local_or_hosted": "local",
  "cycle_checks": [
    {
      "kind": "cycle",
      "claim": "Scheduled or looping main behavior",
      "source": "repository entry points",
      "input": "source inspection",
      "expected": "identify the product trigger",
      "verdict": "yes",
      "outcome": "Inspected README.md (Installation, Configure an MCP client, Sessions/artifacts, Run from source) and the four console entry points (mcp-neko-server, mcp-maboss-server, mcp-physicell-server, mcp-biomass-server). They serve MCP over stdio and expose no cron, loop, webhook, --once or --now trigger. The only CI schedule is in .github/workflows, which is not a product cycle.",
      "evidence": "Inspected README.md (Installation, Configure an MCP client, Sessions/artifacts, Run from source) and the four console entry points (mcp-neko-server, mcp-maboss-server, mcp-physicell-server, mcp-biomass-server). They serve MCP over stdio and expose no cron, loop, webhook, --once or --now trigger. The only CI schedule is in .github/workflows, which is not a product cycle.",
      "command": ""
    }
  ],
  "claims": [
    {
      "kind": "claim",
      "claim": "Each server can maintain multiple isolated modelling sessions; a MaBoSS session is created and its label is returned",
      "source": "Each server can maintain multiple isolated modelling sessions.",
      "input": "{\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass-claim-5521\"}}",
      "expected": "session created with that label returned",
      "command": "<guest-path> tools/call {\"tool\": \"create_session\", \"arguments\": {\"label\": \"coldpass-claim-5521\"}}",
      "verdict": "yes",
      "outcome": "Real input produced the expected result: coldpass-claim-5521",
      "evidence": "\u2026coldpass-claim-5521) (set as default)\", \"type\": \"text\"}], \"isError\": false, \"structuredContent\": {\"result\": \"Session created: 36fd9abe-31c8-44f2-9447-3f8f4c514711 (coldpass-claim-5521) (set as default)\"}}",
      "source_checked": true,
      "source_file": "README.md"
    }
  ],
  "claims_note": null,
  "example_checks": [],
  "does_what_it_says": "yes",
  "maintenance": {
    "last_commit_at": "2026-10-28T07:04:28Z",
    "commits_90d": 105,
    "merged_prs_90d": 13,
    "open_issues": 0,
    "open_prs": 0,
    "reply_share": 0.75,
    "reply_threads": 4,
    "median_reply_hours": 56.5,
    "last_release_at": "2026-10-22T11:54:36Z",
    "archived": false,
    "verdict": "maintained",
    "note": "actively maintained: last commit 0 days ago; 105 commits and 13 merged PRs in 90 days; 0 open issues, 0 open PRs; 3 of 4 recent threads got a maintainer reply, median first reply 56.5h; latest release 2026-10-22"
  },
  "maintenance_verdict": "maintained",
  "maintenance_note": "actively maintained: last commit 0 days ago; 105 commits and 13 merged PRs in 90 days; 0 open issues, 0 open PRs; 3 of 4 recent threads got a maintainer reply, median first reply 56.5h; latest release 2026-10-22",
  "maintained": "active",
  "maintained_note": "last commit 0 days ago; 0 open issues, 2 answered or closed",
  "last_commit_at": "2026-10-28T07:05:58Z",
  "last_release_at": "2026-10-22T11:54:36Z",
  "open_issues": 0,
  "answered_issues": 2,
  "platforms_claimed": [
    "linux",
    "mac",
    "windows"
  ],
  "topic": "mcp-server",
  "agent_interfaces": [
    {
      "interface": "mcp",
      "evidence": "independent checker",
      "observed": true,
      "operation_checked": true
    }
  ],
  "agent_interfaces_note": "README metadata is a discovery hint, not pinned documentation proof. Observed interfaces were exercised in this run. An empty list means unknown.",
  "mcp_context": {
    "tool_count": 26,
    "schema_bytes": 74564,
    "tokens_approx": 18641,
    "estimate_method": "ceil(compact UTF-8 tools/list JSON bytes / 4)",
    "scope": "returned tools/list page only; excludes client framing and tool results"
  },
  "tested_at": "2026-10-28T08:43:06.415758+00:00",
  "tested_commit": "d9079ee2eb8965d27939631da98117abe774091b",
  "tested_with": {
    "agent": "claude-code",
    "agent_version": "2.1.310 (Claude Code)",
    "model": "claude-haiku-5-5",
    "model_route": "claude-haiku-5-5",
    "reasoning": "low",
    "os": "linux",
    "backend": "hyperv",
    "transport": "mcp-assigned-vm"
  },
  "setup_identity": {
    "repo": "marcorusc/mcp-biomodelling-servers",
    "source": "https://github.com/marcorusc/mcp-biomodelling-servers",
    "commit": "d9079ee2eb8965d27939631da98117abe774091b",
    "source_revision": null,
    "os": "linux",
    "architecture": null,
    "backend": "hyperv",
    "model": "claude-haiku-5-5",
    "model_version": "claude-haiku-5-5",
    "agent_execution": "native_agent",
    "agent_runtime": "claude-code",
    "agent_runtime_version": "2.1.310 (Claude Code)",
    "tool_transport": "mcp-assigned-vm",
    "runtime": null,
    "runtime_version": null,
    "runtime_revision": null,
    "sandbox_source": null,
    "guest_setup": null,
    "source_pin": {
      "commit": "d9079ee2eb8965d27939631da98117abe774091b",
      "url": "https://github.com/marcorusc/mcp-biomodelling-servers"
    },
    "platform_details": {
      "os": "linux",
      "backend": "hyperv"
    },
    "platform_conflicts": null,
    "reasoning": "low",
    "service_tier": null,
    "resources": {
      "cpus": 2,
      "memory_mib": 4096,
      "disk_mib": 32768
    },
    "operation": "Install mcp-biomodelling-servers from the source checkout and drive the MaBoSS MCP server over stdio: call create_session with a label and read the returned session ID and label.",
    "operation_scope": "product operation",
    "hosting": null,
    "kind": "mcp",
    "test_version": "readme-2d57868128a84902c09a58991c46c5fe288928e55b1de8282ab5003e13159c2f",
    "evidence_version": null
  },
  "other_model": null,
  "other_run_id": null,
  "models_agree": null,
  "furthest_model": null,
  "transcript_url": "/transcripts/marcorusc--mcp-biomodelling-servers-claude-haiku-5-5-1793176561604258445.txt",
  "report_url": "/reports/marcorusc--mcp-biomodelling-servers-claude-haiku-5-5-1793176561604258445.json"
}