Tools

OpenAI's coding agent that runs locally, written in Rust: reads and writes code and runs commands inside an OS-level sandbox. Sign in with a ChatGPT plan or use an API key.

OpenAI's open-source general-purpose speech recognition model. The whisper command transcribes many languages, translates foreign speech into English and writes subtitle files. Needs FFmpeg; faster with a GPU.

CLI and library for evaluating and red-teaming LLM apps: compare prompts and model outputs in bulk, scan for security vulnerabilities and plug into CI/CD, with evals running locally. Now part of OpenAI and still open source under MIT.

OpenAI's official Codex plugin that guides sequencing analysis from BCL/FASTQ: QC, RNA-seq differential expression, single-cell, variant calling and metagenomics, favoring nf-core and other public pipelines with reproducible run logs. Checks for local tools first. Research use only.

Creates, edits and validates reproducible Python and SQL Jupyter notebooks: organizes cells as reports or tutorials, checks conclusions against actual output and reruns top to bottom before handoff. Maintained by OpenAI in the Data Analytics plugin of openai/plugins.

OpenAI's official Codex plugin that uses the local API of the Zotero desktop app to search your library, export BibTeX, insert citations into LaTeX or Markdown drafts, and import new references after you confirm. Requires Zotero desktop.

OpenAI's official life-science skills: 49 skills query public databases such as UniProt, ClinVar, gnomAD and AlphaFold through Python scripts, with a router skill that breaks down questions, normalizes entities and compiles sourced evidence. Written mainly for Codex.

OpenAI's official Codex plugin with about 50 skills that route questions to genetics, omics, pathway, protein structure, chemistry and clinical evidence sources, can split the work across parallel subagents, and synthesize sourced conclusions.

Build with OpenAI best practices inside Codex: call the OpenAI API, build and deploy agents with the Agents SDK, create ChatGPT apps and prepare submission materials, and create API keys directly. Maintained by OpenAI; Codex only.

Turns articles, reports, papers or notes into a .pptx of full-slide images with speaker notes, in 12 styles such as lectures and thesis defenses; slide text is not editable. Needs Python 3; uses Codex's built-in image generation, or an OpenAI-compatible image API key in Claude Code.

Open-source alternative to NotebookLM's podcast feature: turns web pages, PDFs, images, YouTube videos or text into two-host conversational audio, useful for lecture notes or articles. Uses Gemini and OpenAI API keys by default, or local models plus free Edge TTS.

Turns a paper's method description (text or PDF) or data files into publication-ready diagrams and plots, with several AI reviewer roles refining each figure. Needs an OpenAI or Gemini API key (billed per image), Python and uv. A community reimplementation, not by the original paper's authors.

AI agents collaborate via the ADDIE instructional design model: enter a course name to get a syllabus, LaTeX slides, lecture scripts and assessments, convertible to editable PPTX. Open-source code for an EACL 2026 paper; needs an OpenAI API key, LaTeX for PDFs and Node.js for PPTX.

Microsoft Translator's translation quality tool: GPT scores each sentence using MQM error categories or a direct score; --list_mqm_errors shows error types and severity. Needs line-aligned source and target files, Python and an OpenAI or Azure OpenAI key (paid); a translator should still review.