Public record
Software health reportschema 0.11.0 · metrics 1.13.0 · 2026-07-14 18:16 UTC

intermine / bluegenes-tool-cytoscape

Thin wrapper around the cytoscape-intermine library to present intermine gene & protein interaction networks in bluegenes

HTML · JavaScriptCustom license★ 1 star⑂ 0 forkssince Aug 2018View on GitHub ↗

intermine/bluegenes-tool-cytoscape holds a health index of 21 out of 100, placing it in the Critical band. It scores highest on Sustainability & Governance (38/100) and lowest on Vitality (1/100). It was last updated 1320 days ago. A single contributor accounts for most of its recent work.

21
overall / 100
Critical

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At risk ceiling of 49. AI Readiness sits outside the overall score.

21
Excellent85-100Exemplary; meets essentially all checked criteria
Good70-84Healthy; minor gaps
Moderate50-69Acceptable with notable gaps; review recommended
At risk30-49Significant weaknesses; adoption warrants caution
Critical1-29Severe problems (abandoned, single-maintainer, no hygiene)
VitalityCommunity &AdoptionSustainability &GovernanceEngineeringQualitySecurityAI Readiness

Score profile

Each axis is a category. The shape matters more than the average — a healthy subject fills the whole shape, while a spike-and-crater profile means strength in one dimension is masking risk in another.

Ownership

InterMineOrganization
27 followers185 public repossince Jan 2010

This repository is backed by an organization — shared, accountable stewardship that can outlive any single maintainer.

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
npm@intermine/bluegenes-cytoscape-interaction-network-viewer2.0.211361912 days ago

Metrics by category

Vitality

Is the project alive — is code being written and are releases shipping?

1Critical · 22% of overall
How it's scored
0/36Push recency — last push 1,320 days ago
0/36Commit cadence — 0/52 weeks with commits
0/18Commit volume — 0 commits in the last year
0/10OpenSSF Scorecard: Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
Inputs used
commits_last_year0
human_commit_share
days_since_last_push1,320
active_weeks_last_year0
How it's scored
0/27Ships releases — no releases published
0/36Release recency — no releases
0/27Release cadence — no releases
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count0
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: Signed-Releases. Remaining weights renormalized.

Community & Adoption

Does the project have users, downloads, attention, and a welcoming setup for contributors?

26Critical · 18% of overall
How it's scored
0/60Stars — 1 stars
0/25Forks — 0 forks
5.8/15Watchers — 12 watchers
Inputs used
forks0
stars1
watchers12
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history
How it's scored
22.5/22.5README
16.9/22.5License — license file present, not a recognized license
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
has_contributingno
has_issue_templateno
has_code_of_conductno
has_pull_request_templateno
How it's scored
27.4/80Monthly downloads — 113 downloads/month across npm
0/20Registry dependents — not reported by this ecosystem
Inputs used
packages@intermine/bluegenes-cytoscape-interaction-network-viewer
dependents
ecosystemsnpm
total_downloads
monthly_downloads113
Excluded from scoring (no data or not applicable): Registry dependents. Remaining weights renormalized.

Sustainability & Governance

Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?

38At risk · 24% of overall
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
9/22.5Commit distribution — top contributor authored 60% of commits
2.7/13.5Contributor breadth — 2 contributors
3/10OpenSSF Scorecard: Contributors — project has 1 contributing companies or organizations -- score normalized to 3
Inputs used
bus_factor1
contributors_sampled2
top_contributor_share0.6
How it's scored
0/46.8Issue resolution — 0% of issues closed
0/38.3PR acceptance — 0/4 decided PRs merged
0/15OpenSSF Scorecard: Code-Review — Found 0/10 approved changesets -- score normalized to 0
Inputs used
merged_prs0
open_issues1
closed_issues0
issue_closed_ratio0
closed_unmerged_prs4
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain
10.4/25Owner reach — 27 followers of intermine
25/25Track record — 185 public repos, account ~16 yr old
Inputs used
followers27
owner_typeOrganization
is_verified
owner_loginintermine
public_repos185
account_age_days6,029
How it's scored
25/25Published & resolvable — 1 package(s) on npm
4/35Publish recency — latest publish 1,912 days ago
20/20Version history — 6 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packages@intermine/bluegenes-cytoscape-interaction-network-viewer
ecosystemsnpm
any_deprecatedno
min_days_since_publish1,912

Engineering Quality

Are baseline engineering and documentation practices in place?

21Critical · 20% of overall
How it's scored
0/24CI workflows
0/24Tests present
0/16Linter config
0/9.6Pre-commit hooks
0/6.4.editorconfig
0/20OpenSSF Scorecard: CI-Tests — no data
Inputs used
has_cino
has_testsno
has_editorconfigno
has_linter_configno
has_precommit_configno
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: CI-Tests. Remaining weights renormalized.

Documentation

50Moderate
How it's scored
30/30README
0/25Documentation directory
0/15Documentation / homepage site
10/10Repository description
10/10Topics — 1 topics
0/10Wiki
Inputs used
topicsbluegenes-tool
has_wikino
homepage
has_readmeyes
has_docs_dirno
has_descriptionyes

Security

Are visible security and supply-chain practices strong, without unresolved high-risk jurisdiction exposure?

16Critical · 16% of overall
How it's scored
7.5/7.5Binary-Artifacts — no binaries found in the repo
0/7.5Branch-Protection — branch protection not enabled on development/release branches
0/2.5CI-Tests — no data
0/2.5CII-Best-Practices — no effort to earn an OpenSSF best practices badge detected
0/7.5Code-Review — Found 0/10 approved changesets -- score normalized to 0
0.8/2.5Contributors — project has 1 contributing companies or organizations -- score normalized to 3
0/10Dangerous-Workflow — no data
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.2/2.5License — license file detected
0/7.5Maintained — 0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
0/5Packaging — no data
0/5Pinned-Dependencies — no data
0/5SAST — no SAST tool detected
0/5Security-Policy — security policy file not detected
0/7.5Signed-Releases — no data
0/7.5Token-Permissions — no data
0/7.5Vulnerabilities — 61 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated12
scorecard_versionv5.5.0
checks_inconclusive6
scorecard_aggregate1.6
Excluded from scoring (no data or not applicable): ci_tests, dangerous_workflow, packaging, pinned_dependencies, signed_releases, token_permissions. Remaining weights renormalized.

AI Readiness

How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score.

17Critical · 0% of overall
How it's scored
0/45Agent instructions — no CLAUDE.md / AGENTS.md / editor rules
0/15Machine-readable docs (llms.txt)
0/40Legible commit history — no data
Inputs used
has_llms_txtno
legible_history_share
agent_instruction_files
agent_instruction_max_bytes
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.
How it's scored
0/18One-command bootstrap
0/22Automated tests
0/11Lint / format config
0/11Static type checking
10/10Reproducible environment — lockfile
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — no data
Inputs used
has_nixno
has_testsno
lockfilespackage-lock.json
has_dockerfileno
typed_languageno
bootstrap_files
has_devcontainerno
has_linter_configno
typecheck_configs
agent_commit_share
toolchain_manifests
dependency_bot_commit_share
Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance, OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.
How it's scored
0/45Type-checkable code — HTML without a type-check config
55/55Manageable file sizes — 0/2 source files over 60KB
Inputs used
primary_languageHTML
largest_source_bytes829
source_files_sampled2
oversized_source_files0

Key facts

1GitHub stars
2contributors
0commits, last 12 months
1,320days since last push
0releases
1bus factor
1open issues
npmpackage ecosystems

More detail

OpenSSF Scorecard 1.6 / 10
1.6aggregate

Independent, tool-agnostic security assessment from the open-source OpenSSF Scorecard. Each check rewards a security practice, not a specific vendor's tool. Checks Scorecard could not determine are marked n/a and excluded from the security score (never counted as zero).Scorecard v5.5.0 · 2026-07-14 18:15 UTC

10Binary-Artifactsno binaries found in the repo
0Branch-Protectionbranch protection not enabled on development/release branches
n/aCI-Testsno pull request found
0CII-Best-Practicesno effort to earn an OpenSSF best practices badge detected
0Code-ReviewFound 0/10 approved changesets -- score normalized to 0
3Contributorsproject has 1 contributing companies or organizations -- score normalized to 3
n/aDangerous-Workflowno workflows found
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
9Licenselicense file detected
0Maintained0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0
n/aPackagingpackaging workflow not detected
n/aPinned-Dependenciesno dependencies found
0SASTno SAST tool detected
0Security-Policysecurity policy file not detected
n/aSigned-Releasesno releases found
n/aToken-PermissionsNo tokens found
0Vulnerabilities61 existing vulnerabilities detected
Direct dependencies 5
RegistryPackageVersion constraintManifest
npm@intermine/cytoscape-intermine^1.1.4package.json
npmcytoscape^3.18.2package.json
npmes6-promise^4.2.8package.json
npmserve^9.6.0package.json
npmunderscore^1.13.1package.json
All dependencies 503

Full resolved dependency set from the GitHub dependency graph: 5 direct and 498 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
npm@intermine/cytoscape-intermine1.1.4direct
npmcytoscape3.18.2direct
npmes6-promise4.2.8direct
npmserve9.6.0direct
npmunderscore1.13.1direct
npm@webassemblyjs/ast1.9.0indirect
npm@webassemblyjs/floating-point-hex-parser1.9.0indirect
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npm@webassemblyjs/helper-code-frame1.9.0indirect
npm@webassemblyjs/helper-fsm1.9.0indirect
npm@webassemblyjs/helper-module-context1.9.0indirect
npm@webassemblyjs/helper-wasm-bytecode1.9.0indirect
npm@webassemblyjs/helper-wasm-section1.9.0indirect
npm@webassemblyjs/ieee7541.9.0indirect
npm@webassemblyjs/leb1281.9.0indirect
npm@webassemblyjs/utf81.9.0indirect
npm@webassemblyjs/wasm-edit1.9.0indirect
npm@webassemblyjs/wasm-gen1.9.0indirect
npm@webassemblyjs/wasm-opt1.9.0indirect
npm@webassemblyjs/wasm-parser1.9.0indirect
npm@webassemblyjs/wast-parser1.9.0indirect
npm@webassemblyjs/wast-printer1.9.0indirect
npm@xtuc/ieee7541.2.0indirect
npm@xtuc/long4.2.2indirect
npm@zeit/schemas2.1.1indirect
npmacorn6.4.2indirect
npmajv6.12.6indirect
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npmajv-errors1.0.1indirect
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npmamdefine1.0.1indirect
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npmappend-buffer1.0.2indirect
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npmarch2.1.1indirect
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            "notes": [],
            "value": 44,
            "inputs": {
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              "has_contributing": false,
              "has_issue_template": false,
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                "key": "license",
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        "key": "governance",
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                "key": "openssf_scorecard_contributors",
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                "points": 3,
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                "max_points": 10
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              "issue_closed_ratio": 0,
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            "key": "stewardship",
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            "notes": [],
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              "is_verified": null,
              "owner_login": "intermine",
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              "account_age_days": 6029
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            "components": [
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                "key": "owner_reach",
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                "key": "track_record",
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                "details": [
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            "notes": [],
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                "key": "not_deprecated",
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            ]
          }
        ],
        "description": "Will the project survive its people — bus factor, responsiveness, who backs it, and package upkeep?"
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              {
                "key": "dependency_update_tool",
                "name": "Dependency-Update-Tool",
                "detail": "no update tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "fuzzing",
                "name": "Fuzzing",
                "detail": "project is not fuzzed",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "license",
                "name": "License",
                "detail": "license file detected",
                "points": 2.2,
                "status": "partial",
                "details": [],
                "max_points": 2.5
              },
              {
                "key": "maintained",
                "name": "Maintained",
                "detail": "0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              },
              {
                "key": "packaging",
                "name": "Packaging",
                "detail": "packaging workflow not detected",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "pinned_dependencies",
                "name": "Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 5
              },
              {
                "key": "sast",
                "name": "SAST",
                "detail": "no SAST tool detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "security_policy",
                "name": "Security-Policy",
                "detail": "security policy file not detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 5
              },
              {
                "key": "signed_releases",
                "name": "Signed-Releases",
                "detail": "no releases found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "token_permissions",
                "name": "Token-Permissions",
                "detail": "No tokens found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 7.5
              },
              {
                "key": "vulnerabilities",
                "name": "Vulnerabilities",
                "detail": "61 existing vulnerabilities detected",
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 7.5
              }
            ]
          },
          {
            "key": "high_risk_jurisdiction_exposure",
            "band": "excellent",
            "name": "High-Risk Jurisdiction Exposure",
            "note": "Only high-confidence self-published location evidence affects this multiplier. Ambiguous matches are review-only; country evidence is not proof of nationality, citizenship, legal registration, malicious intent, or sanctions status.",
            "notes": [
              {
                "code": "jurisdiction_evidence_limits",
                "params": {}
              }
            ],
            "value": 100,
            "inputs": {
              "meaning": "self-published location evidence; not nationality or citizenship",
              "red_flag": false,
              "exposures": [],
              "policy_countries": [
                "Russia",
                "Iran",
                "North Korea"
              ],
              "review_only_matches": 0,
              "assessed_self_published_locations": 3
            },
            "components": [
              {
                "key": "policy_exposure_multiplier",
                "name": "Policy exposure multiplier",
                "detail": "no confirmed policy-scope location match",
                "points": 100,
                "status": "met",
                "details": [
                  {
                    "code": "jurisdiction_no_match",
                    "params": {}
                  }
                ],
                "max_points": 100
              }
            ]
          }
        ],
        "description": "Are visible security and supply-chain practices strong, with no malicious dependency and no unresolved high-risk jurisdiction exposure?"
      },
      {
        "key": "ai_readiness",
        "band": "critical",
        "name": "AI Readiness",
        "value": 17,
        "weight": 0,
        "metrics": [
          {
            "key": "ai_agent_context",
            "band": "critical",
            "name": "Agent context & guidance",
            "note": "Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "legible_commit_history"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 1,
            "inputs": {
              "has_llms_txt": false,
              "legible_history_share": null,
              "agent_instruction_files": [],
              "agent_instruction_max_bytes": null
            },
            "components": [
              {
                "key": "agent_instructions",
                "name": "Agent instructions",
                "detail": "no CLAUDE.md / AGENTS.md / editor rules",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_agent_instructions",
                    "params": {}
                  }
                ],
                "max_points": 45
              },
              {
                "key": "machine_readable_docs_llms_txt",
                "name": "Machine-readable docs (llms.txt)",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 15
              },
              {
                "key": "legible_commit_history",
                "name": "Legible commit history",
                "detail": "no data",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 40
              }
            ]
          },
          {
            "key": "ai_verify_loop",
            "band": "critical",
            "name": "Verify loop (build / test / typecheck)",
            "note": "Excluded from scoring (no data or not applicable): Demonstrated agent practice, Automated maintenance, OpenSSF Scorecard: Pinned-Dependencies. Remaining weights renormalized.",
            "notes": [
              {
                "code": "excluded_no_data",
                "params": {
                  "components": [
                    "demonstrated_agent_practice",
                    "automated_maintenance",
                    "openssf_scorecard_pinned_dependencies"
                  ]
                }
              },
              {
                "code": "weights_renormalized",
                "params": {}
              }
            ],
            "value": 14,
            "inputs": {
              "has_nix": false,
              "has_tests": false,
              "lockfiles": [
                "package-lock.json"
              ],
              "has_dockerfile": false,
              "typed_language": false,
              "bootstrap_files": [],
              "has_devcontainer": false,
              "has_linter_config": false,
              "typecheck_configs": [],
              "agent_commit_share": null,
              "toolchain_manifests": [],
              "dependency_bot_commit_share": null
            },
            "components": [
              {
                "key": "one_command_bootstrap",
                "name": "One-command bootstrap",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 18
              },
              {
                "key": "automated_tests",
                "name": "Automated tests",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 22
              },
              {
                "key": "lint_format_config",
                "name": "Lint / format config",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "static_type_checking",
                "name": "Static type checking",
                "detail": null,
                "points": 0,
                "status": "missed",
                "details": [],
                "max_points": 11
              },
              {
                "key": "reproducible_environment",
                "name": "Reproducible environment",
                "detail": "lockfile",
                "points": 10,
                "status": "met",
                "details": [
                  {
                    "code": "file_list",
                    "params": {
                      "files": "lockfile"
                    }
                  }
                ],
                "max_points": 10
              },
              {
                "key": "demonstrated_agent_practice",
                "name": "Demonstrated agent practice",
                "detail": "no data",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              },
              {
                "key": "automated_maintenance",
                "name": "Automated maintenance",
                "detail": "no data",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 8
              },
              {
                "key": "openssf_scorecard_pinned_dependencies",
                "name": "OpenSSF Scorecard: Pinned-Dependencies",
                "detail": "no dependencies found",
                "points": 0,
                "status": "excluded",
                "details": [
                  {
                    "code": "no_data",
                    "params": {}
                  }
                ],
                "max_points": 10
              }
            ]
          },
          {
            "key": "ai_code_legibility",
            "band": "moderate",
            "name": "Code legibility for models",
            "note": null,
            "notes": [],
            "value": 55,
            "inputs": {
              "primary_language": "HTML",
              "largest_source_bytes": 829,
              "source_files_sampled": 2,
              "oversized_source_files": 0
            },
            "components": [
              {
                "key": "type_checkable_code",
                "name": "Type-checkable code",
                "detail": "HTML without a type-check config",
                "points": 0,
                "status": "missed",
                "details": [
                  {
                    "code": "no_typecheck_config_language",
                    "params": {
                      "language": "HTML"
                    }
                  }
                ],
                "max_points": 45
              },
              {
                "key": "manageable_file_sizes",
                "name": "Manageable file sizes",
                "detail": "0/2 source files over 60KB",
                "points": 55,
                "status": "met",
                "details": [
                  {
                    "code": "oversized_source_files",
                    "params": {
                      "kb": 60,
                      "sampled": 2,
                      "oversized": 0
                    }
                  }
                ],
                "max_points": 55
              }
            ]
          }
        ],
        "description": "How well is the repo equipped to be developed and maintained with AI coding agents? An independent, experimental badge — weight 0.0, so it is surfaced on its own and does not affect the overall health score."
      }
    ],
    "metrics_version": "1.13.0"
  },
  "warnings": [],
  "report_type": "repository",
  "generated_at": "2026-07-14T18:16:01.377956Z",
  "schema_version": "0.11.0",
  "badge_url": "https://raw.githubusercontent.com/inspect-software/badges/main/v1/i/intermine/bluegenes-tool-cytoscape.svg",
  "full_name": "intermine/bluegenes-tool-cytoscape",
  "license_state": "custom",
  "license_spdx": null
}

Scores are signals, not warranties. They reflect publicly visible practices on GitHub — not a code audit, and not a security guarantee.

Missing data is excluded and weights renormalized, never scored as zero. Methodology is versioned and open: metrics v1.13.0, schema v0.11.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statisticsnpm.