Versioned security assessment

Report ID: SA-B7B8B37E

6/30/2026, 5:44:45 AM

arboreto security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
arboreto
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/arboreto
Coverage
5 Files scanned · 875 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 external command and weak cryptography patterns, but review found these are false positives from Markdown code fences, algorithm names, and scientific terminology. The real risks are legitimate workflow risks: a helper script reads and writes user-specified local files, and distributed Dask examples can connect to remote scheduler endpoints.

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

5 Files scanned · 875 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 1 evidence location

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 3 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
references/distributed_computing.md:107-124SKILL.md:108-114
Remote Dask Scheduler Connection Guidance
The skill documents connecting Arboreto jobs to a Dask scheduler address for cluster execution. This is legitimate for distributed bioinformatics work, but expression data may be transmitted to remote workers if users choose an untrusted scheduler.
The files explicitly show Dask scheduler addresses and client connections. No malicious endpoint is present, but the data movement risk is real when users connect to remote infrastructure.
RISK-002 Medium
scripts/basic_grn_inference.py:34-59scripts/basic_grn_inference.py:70-96
User-Specified Local File Read and Write
The bundled script accepts input, output, and transcription factor file paths, then reads expression data and writes network results. This is expected functionality, but users should run it only on intended files and trusted datasets.
The script directly reads paths from command line arguments and writes the requested output path. This is not malicious, but it is confirmed filesystem access.

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 (3)
Low
SKILL.md:20-22references/algorithms.md:29-37references/basic_inference.md:57-77references/distributed_computing.md:107-115
External Command Findings Are Markdown Code Fence False Positives
The reported Ruby or shell backtick detections occur on fenced Markdown examples for Bash or Python usage. They are documentation delimiters and example commands, not hidden command execution inside skill code.
The reported locations are Markdown fences or examples displayed to the user. There is no Ruby code or dynamic shell execution in those lines.
Low
references/algorithms.md:1-3references/basic_inference.md:108-116references/distributed_computing.md:193-196scripts/basic_grn_inference.py:66-69
Weak Cryptography Findings Are Scientific Terminology False Positives
The high severity weak cryptography alerts map to words such as algorithm, Random Forest, network, or scheduling in scientific documentation. No cryptographic primitive, password hashing, encryption, or signature implementation was found.
Reviewed context contains bioinformatics and machine learning terms, not cryptographic code. The static pattern appears to have matched broad keywords outside a security context.
Low
references/distributed_computing.md:107-124references/distributed_computing.md:158-162
Hardcoded Network Values Are Documentation Examples
The hardcoded IP address, localhost dashboard URL, and scheduler address are examples for Dask cluster setup. They do not contact an external service unless a user applies them in their own environment.
The network indicators are presented as Dask setup examples and dashboard documentation. No automatic network request or data exfiltration logic was found in the skill files.

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