Public record
Software health reportschema 0.11.0 · metrics 2.10.0 · 2026-07-17 03:09 UTC

sbrg / ssbio

A Python framework for structural systems biology

PythonMIT★ 109 stars⑂ 30 forkssince Jan 2016View on GitHub ↗
KindLibraryhow this is determined
#systems-biology#protein-structure#structural-biology#constraint-based-modeling#cobrapy#structural-systems-biology

sbrg/ssbio holds a health index of 36 out of 100, placing it in the Weak band. It scores highest on Engineering Quality (58/100) and lowest on Security (21/100). It was last updated 2047 days ago. A single contributor accounts for most of its recent work.

36
overall / 100
Weak

Software health index

Metrics are grouped into weighted categories on one standardized 1–100 scale. Overall starts as their weighted mean, calibrated against the distribution of the public record so bands carry percentile meaning; when public evidence triggers the High-Risk Jurisdiction Policy, the rating is adjusted and receives an At Risk ceiling of 34.

36
Exceptional93-100The record's top tier (≈ top 5%); essentially all checked criteria met
Excellent80-92Strong across the board; minor gaps
Good65-79Healthy; gaps are limited and manageable
Moderate50-64Acceptable with notable gaps; review recommended
Weak35-49Material weaknesses across several areas
At Risk20-34Significant weaknesses; adoption warrants caution
Critical1-19Severe 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.

The weighted overall 41 is calibrated to 36 on the published index scale (record calibration 2026-08-02).

Ownership

Systems Biology Research GroupOrganization
67 followers85 public repossince Apr 2013

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

Package ecosystems

RegistryPackageVersionDownloads / moVersionsLast publish
PyPIssbio0.9.9.8.post1474202690 days ago

Metrics by category

Vitality

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

21At Risk · 21% of overall

Development activity

1Critical
How it's scored
0/36Push recency — last push 2,047 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_push2,047
active_weeks_last_year0

Release discipline

52Moderate
How it's scored
27/27Ships releases — 14 releases published
0/36Release recency — latest release 2,690 days ago
19.8/27Release cadence — a release every ~51.4 days
0/10OpenSSF Scorecard: Signed-Releases — no data
Inputs used
releases_count14
latest_release_tagv0.9.9.8.post1
releases_from_tagsno
days_since_latest_release2,690
mean_days_between_releases51.4
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?

50Moderate · 17% of overall

Popularity & adoption

52Moderate
How it's scored
33/60Stars — 109 stars
12.2/25Forks — 30 forks
6.5/15Watchers — 16 watchers
Inputs used
forks30
stars109
watchers16
growth_stateunverified
growth_factor_pct100
growth_unverified_reasonno_history

Community health

50Moderate
How it's scored
22.5/22.5README
22.5/22.5License — recognized license (MIT)
0/18CONTRIBUTING guide
0/13.5Code of conduct
0/7.2Issue template
0/6.3PR template
Inputs used
has_readmeyes
has_licenseyes
readme_badges—
has_contributingno
has_issue_templateno
has_code_of_conductno
readme_badge_services—
has_pull_request_templateno

Ecosystem adoption (downloads)

45Weak
How it's scored
35.7/80Monthly downloads — 474 downloads/month across pypi
0/20Registry dependents — not reported by this ecosystem
Inputs used
packagesssbio
dependents—
ecosystemspypi
total_downloads—
monthly_downloads474
unverified_packages_excluded—
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?

52Moderate · 23% of overall

Maintainer resilience (bus factor)

16Critical
How it's scored
9/54Bus factor — 1 contributor(s) cover half of all commits
0/22.5Commit distribution — top contributor authored 100% of commits
1.4/13.5Contributor breadth — 1 contributors
6/10OpenSSF Scorecard: Contributors — project has 2 contributing companies or organizations -- score normalized to 6
Inputs used
bus_factor1
contributors_sampled1
top_contributor_share1

Issue & PR responsiveness

48Weak
How it's scored
12/42Issue resolution — 29% of issues closed
30/30PR acceptance — 16/16 decided PRs merged
0/13Newcomer PR acceptance — no first-time contributor's PR decided in 30d
0/15OpenSSF Scorecard: Code-Review — Found 0/30 approved changesets -- score normalized to 0
Inputs used
merged_prs16
open_issues30
closed_issues12
prs_merged_7d—
prs_decided_7d—
prs_merged_30d—
prs_decided_30d—
issue_closed_ratio0.286
closed_unmerged_prs0
first_time_authors_30d—
first_time_prs_merged_30d—
first_time_prs_decided_30d—
Excluded from scoring (no data or not applicable): Newcomer PR acceptance. Remaining weights renormalized.

Ownership & stewardship

85Excellent
How it's scored
30/30Ownership backing — organization-owned
0/20Verified domain — verified-domain status not read for this organization
13.2/25Owner reach — 67 followers of SBRG
25/25Track record — 85 public repos, account ~13 yr old
Inputs used
followers67
owner_typeOrganization
is_verified—
owner_loginSBRG
public_repos85
account_age_days4,832
Excluded from scoring (no data or not applicable): Verified domain. Remaining weights renormalized.

Package maintenance

69Good
How it's scored
25/25Published & resolvable — 1 package(s) on pypi
4/35Publish recency — latest publish 2,690 days ago
20/20Version history — 20 published versions
20/20Not deprecated — active, not deprecated or yanked
Inputs used
packagesssbio
ecosystemspypi
any_deprecatedno
min_days_since_publish2,690

Engineering Quality

Are baseline engineering and documentation practices in place?

58Moderate · 19% of overall

Engineering practices

30At Risk
How it's scored
0/24CI workflows
24/24Tests 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_testsyes
has_editorconfigno
has_linter_configno
has_precommit_configno
Excluded from scoring (no data or not applicable): OpenSSF Scorecard: CI-Tests. Remaining weights renormalized.

Documentation

100Exceptional
How it's scored
30/30README
25/25Documentation directory
15/15Documentation / homepage site — http://ssbio.readthedocs.io/en/latest/
10/10Repository description
10/10Topics — 6 topics
10/10Wiki
Inputs used
topicssystems-biology, protein-structure, structural-biology, constraint-based-modeling, cobrapy, structural-systems-biology
has_wikiyes
homepagehttp://ssbio.readthedocs.io/en/latest/
docs_sitehttp://ssbio.readthedocs.io/en/latest/
has_readmeyes
has_docs_diryes
has_descriptionyes

Security

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

21At Risk · 16% of overall

Security posture

21At Risk
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 0/30 approved changesets -- score normalized to 0
1.5/2.5Contributors — project has 2 contributing companies or organizations -- score normalized to 6
0/10Dangerous-Workflow — no data
0/7.5Dependency-Update-Tool — no update tool detected
0/5Fuzzing — project is not fuzzed
2.5/2.5License — 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
3/7.5Vulnerabilities — 6 existing vulnerabilities detected
Inputs used
sourceopenssf_scorecard
checks_evaluated12
scorecard_versionv5.5.0
checks_inconclusive6
scorecard_aggregate2.1
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? Carries a deliberately small weight (4%): agent tooling is a real maintenance signal, but a repository with none can still reach 100/100.

46Weak · 4% of overall

Agent context & guidance

1Critical
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
llms_txt_url—
legible_history_share—
agent_instruction_files—
agent_instruction_max_bytes—
Excluded from scoring (no data or not applicable): Legible commit history. Remaining weights renormalized.

Verify loop (build / test / typecheck)

56Moderate
How it's scored
18/18One-command bootstrap — docs/Makefile
22/22Automated tests
0/11Lint / format config
0/11Static type checking
0/10Reproducible environment
0/10Demonstrated agent practice — no data
0/8Automated maintenance — no data
0/10OpenSSF Scorecard: Pinned-Dependencies — no data
Inputs used
has_nixno
has_testsyes
lockfiles—
has_dockerfileno
typed_languageno
bootstrap_filesdocs/Makefile
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.

Code legibility for models

52Moderate
How it's scored
0/45Type-checkable code — Python without a type-check config
52/55Manageable file sizes — 6/111 source files over 60KB
Inputs used
primary_languagePython
largest_source_bytes1,131,457
source_files_sampled111
oversized_source_files6

Machine-readable interfaces

100Exceptional
How it's scored
0/40API schema (OpenAPI/GraphQL/proto) — not applicable to this kind of software
0/20MCP server — not applicable to this kind of software
40/40Runnable examples — notebooks
Inputs used
example_dirsnotebooks
has_mcp_signalno
api_schema_files—
interfaces_expected_of—
Excluded from scoring (no data or not applicable): API schema (OpenAPI/GraphQL/proto), MCP server. Remaining weights renormalized.

Key facts

109GitHub stars
1contributors
0commits, last 12 months
2,047days since last push
14releases
1bus factor
30open issues
PyPIpackage ecosystems

More detail

OpenSSF Scorecard 2.1 / 10
2.1aggregate

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 · 2026-07-17 03:09 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 0/30 approved changesets -- score normalized to 0
6Contributorsproject has 2 contributing companies or organizations -- score normalized to 6
n/aDangerous-Workflowno workflows found
0Dependency-Update-Toolno update tool detected
0Fuzzingproject is not fuzzed
10Licenselicense 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
4Vulnerabilities6 existing vulnerabilities detected
All dependencies 34

Full resolved dependency set from the GitHub dependency graph: 0 direct and 34 indirect (transitive) packages. The transitive closure is complete when the repository commits a lockfile.

RegistryPackageVersionRelation
PyPIawesome-slugify—indirect
PyPIbcbio-gff—indirect
PyPIbeautifulsoup44.5.3indirect
PyPIbiopandas—indirect
PyPIbiopython—indirect
PyPIbioservices—indirect
PyPIcobra—indirect
PyPIdeprecation—indirect
PyPIipykernel—indirect
PyPIipywidgets7.0.0indirect
PyPIjoblib—indirect
PyPIjson-tricks—indirect
PyPIjupyter-contrib-nbextensions—indirect
PyPIlxml—indirect
PyPImatplotlib—indirect
PyPImmtf-python—indirect
PyPImore-itertools—indirect
PyPImsgpack-python—indirect
PyPInbsphinx—indirect
PyPInetworkx—indirect
PyPInglview1.0indirect
PyPInumpy—indirect
PyPIpandas—indirect
PyPIpytest—indirect
PyPIrequests—indirect
PyPIrequests-cache0.4.13indirect
PyPIscipy—indirect
PyPIseaborn—indirect
PyPIsix—indirect
PyPIsphinx—indirect
PyPIsphinx-rtd-theme—indirect
PyPIssbio—indirect
PyPItqdm—indirect
PyPIxmltodict—indirect
Raw JSON report machine-readable

Feedback

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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 v2.10.0, schema v0.11.0 — full methodology · metrics wiki.

How one result sits in the wider record: aggregate statistics — PyPI.