Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Use when the user asks how to build with OpenAI products or APIs and needs up-to-date official documentation with citations, help choosing the latest model for a use case, or explicit GPT-5.4 upgrade and prompt-upgrade guidance; prioritize OpenAI docs MCP tools, use bundled references only as helper context, and restrict any fallback browsing to official OpenAI domains.

Perform language and framework specific security best-practice reviews and suggest improvements. Trigger only when the user explicitly requests security best practices guidance, a security review/report, or secure-by-default coding help. Trigger only for supported languages (python, javascript/typescript, go). Do not trigger for general code review, debugging, or non-security tasks.

Repository-grounded threat modeling that enumerates trust boundaries, assets, attacker capabilities, abuse paths, and mitigations, and writes a concise Markdown threat model. Trigger only when the user explicitly asks to threat model a codebase or path, enumerate threats/abuse paths, or perform AppSec threat modeling. Do not trigger for general architecture summaries, code review, or non-security design work.

Use only when the user explicitly asks to stage, commit, push, and open a GitHub pull request in one flow using the GitHub CLI (`gh`).

Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.

Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.

Prepare meeting materials with Notion context and Codex research; use when gathering context, drafting agendas/pre-reads, and tailoring materials to attendees.

Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.

Persistent browser and Electron interaction through `js_repl` for fast iterative UI debugging.

Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.

Use when Codex is building or iterating on a web game (HTML/JS) and needs a reliable development + testing loop: implement small changes, run a Playwright-based test script with short input bursts and intentional pauses, inspect screenshots/text, and review console errors with render_game_to_text.

Deploy applications and websites to Vercel. Use when the user requests deployment actions like "deploy my app", "deploy and give me the link", "push this live", or "create a preview deployment".