Versioned security assessment

Report ID: SA-FF49DD72

6/30/2026, 6:02:01 AM

bioservices security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
bioservices
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/bioservices
Coverage
8 Files scanned · 3,942 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

2 confirmed security findings require attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported many high-risk patterns, but review found the external command and weak-crypto alerts are false positives caused by Markdown code fences, database names, and scientific terms. The confirmed risks are legitimate helper scripts that contact public bioinformatics services and write user-selected result files, so publication is acceptable with a network and filesystem warning.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

8 Files scanned · 3,942 Lines analyzed

2 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Observed in 4 evidence locations

Network access

May connect to external services.

Observed in 4 evidence locations

Filesystem access

May read or write local files.

Observed in 4 evidence locations

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Not recorded by this audit

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (2)

RISK-001 Medium
scripts/protein_analysis_workflow.py:137-143scripts/protein_analysis_workflow.py:257scripts/compound_cross_reference.py:37scripts/compound_cross_reference.py:237
External Bioinformatics Service Calls
The helper scripts submit protein sequences, identifiers, compound names, and an optional BLAST email address to public BioServices-backed databases. This is expected for the skill, but users should treat submitted research inputs as data shared with third-party scientific services.
Direct API calls are visible in scripts and match the documented BioServices purpose. The risk is data disclosure to external scientific services, not malicious exfiltration.
RISK-002 Medium
scripts/batch_id_converter.py:168-183scripts/batch_id_converter.py:195-197scripts/pathway_analysis.py:173-180scripts/compound_cross_reference.py:284-312
User-Controlled Result File Writes
Command-line helpers write CSV, SIF, text, and detailed pathway files to paths supplied by the user or default output names. This is legitimate export behavior, but it can overwrite files if users choose unsafe paths.
The file writes are explicit and are tied to result export functions. No destructive deletion is present, but output paths are not restricted.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (1)
Low
references/identifier_mapping.md:33-47references/services_reference.md:12-30references/services_reference.md:402-408scripts/protein_analysis_workflow.py:320-327
Static Shell and Crypto Alerts Are False Positives
The reported Ruby backtick, weak cryptography, C2 keyword, reconnaissance, and dynamic-constructor alerts occur in Markdown examples or ordinary bioinformatics vocabulary. No evidence found of shell execution, obfuscation, credential access, or malicious control flow in the reviewed files.
The cited lines show Python documentation examples and GO category text, not executable shell or cryptographic logic. Targeted review did not find matching malicious semantics.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable