OpenAI Codex security directory

Life Sciences NGS Analysis

Published by OpenAI

High risk

Guides Codex through local next-generation sequencing analysis. Inspect sequencing inputs, choose assay-specific workflows and run supported analysis tools. Covers DNA variants, RNA-seq, epigenomics and microbiome analysis with QC reports and logs.

Security assessment

Plutonium assessed this plugin for permissions, capabilities, and security-relevant behavior.

  • Analysis runners launch tokenless local Marimo review applications: Can programmatically control a browser, including navigation, form input, clicks, capture, or page inspection.
  • Runners create and replace analysis workspaces and biological artifacts: Can read, create, or change files on the local filesystem or in a selected project.
  • Can send data to external services: Can send prompts, files, queries, or connected-service data to an external service.
  • Plugin reads local human sequencing and sample metadata: Can read private account, workspace, repository, message, analytics, or file data.
  • NGS workflows execute extensive local pipelines and optional package installation: Can execute code, commands, scripts, unrestricted queries, or dynamic gateway actions.

Available capabilities

This add-on exposes 18 tools or capabilities.

  • ngs-amplicon-microbiome
  • ngs-analysis-router
  • ngs-atacseq-peaks-qc
  • ngs-bcl-to-fastq
  • ngs-bulk-rnaseq
  • ngs-bulk-rnaseq-counts-qc
  • ngs-bulk-rnaseq-differential-expression
  • ngs-chip-cutrun-peaks-qc
  • ngs-dna-germline-variants
  • ngs-dna-somatic-variants
  • ngs-dna-umi-panel-variants
  • ngs-dna-variant-calling
  • ngs-epigenomics-peaks
  • ngs-fastq-qc
  • ngs-runtime-env
  • ngs-scrna-seq
  • ngs-shotgun-metagenomics
  • scrna-seq-qc

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