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Codex MCP Setup

Scibudy exposes a local stdio MCP server named research. Once configured, Codex can call Scibudy tools for search, library creation, ingestion, evidence retrieval, synthesis, and journal-style analysis.

Automatic setup

Use the installer or bootstrap flow:

npx scibudy-install --profile base
scibudy install-codex
codex mcp get research

Or from a source checkout:

scibudy bootstrap --profile base --install-codex
codex mcp get research

scibudy install-codex updates the managed research MCP block in:

~/.codex/config.toml

It points Codex at research-mcp or scibudy-mcp, depending on the installed runtime.

Manual setup

If you do not want Scibudy to edit Codex config automatically, bootstrap without Codex changes:

scibudy bootstrap --profile base --no-install-codex

Then add a research MCP server in Codex that uses:

transport: stdio
command: research-mcp

Use the absolute command path when Codex cannot resolve the command from its login environment.

Verify

codex mcp get research

Expected signals:

  • server name is research
  • transport is stdio
  • command points to research-mcp or scibudy-mcp
  • the server exposes search, open-access, library, analysis, synthesis, and UI tools

For runtime readiness:

scibudy doctor --json
scibudy security-audit

Typical Codex prompts

Search recent literature on posterior calibration in simulation-based inference using research_workflow. Use dry_run=true first.

Use collect_library to build a local library for "Bayesian atmospheric chemistry inverse modeling", then ingest_library and search_library_evidence for "uncertainty calibration".

Run analyze_journal_style for nature-communications with query "atmospheric chemistry Bayesian inference" and summarize the output files.

Troubleshooting

If Codex cannot see the MCP server:

scibudy install-codex
codex mcp get research
scibudy doctor --json

If the command path is missing in an SSH or GUI-launched Codex session, reinstall with Scibudy or edit the MCP block to use an absolute path to research-mcp.