Genome Computer
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Your first walkthrough · Lesson 1 of 3

Open your .genome in Codex

Set up your workspace and verify that Codex can read your files.

5 min read · allow extra time to follow alongCodex

Before you start

  • The Codex desktop app, signed in.
  • Your downloaded .genome bundle. The next lesson also includes a synthetic exercise.

Start by making your files visible to Codex. This lesson uses a folder on your computer; you should finish with a short map of the files the agent can actually read.

1. Put the bundle in its own folder

  • Create a folder named Genome exploration in Finder or File Explorer. Put your downloaded .genome bundle inside it.
  • If your download ends in .tar.gz or .zip, extract the archive first. Open the resulting .genome folder and check that it contains files, rather than another unopened archive.
  • Keep the original download. Save reports outside the bundle so the original data stays easy to identify.

Check your folder

Genome exploration/
└── your-bundle.genome/
    ├── README.md
    ├── manifest.json
    ├── inventory.json
    └── …
Illustrative file map. Filenames vary by bundle version; use the files in your download.

2. Open that folder in Codex

  • Open the desktop app and sign in. Add a local project by selecting the Genome exploration folder you just created.
  • Select that project and start a new Codex chat. Choose the local folder for the task if the app asks where to work.
  • Before sending a question, check that the selected project is Genome exploration. A chat opened in another project will not automatically see this folder.

3. Copy this prompt into the new chat

Inspect the .genome bundle in this project. Read its README, manifest, inventory, and any bundled usage instructions that are present. List the actual paths you can access and explain which files are useful for variant lookup, annotations, sources, and quality information. Flag missing, unreadable, or unsupported files. Do not make biological claims or modify the bundle. Finish with a short file map.

Check the response

File                         What it contains
manifest.json                Bundle version and metadata
inventory.json               Inventory of bundle contents
variants.parquet/            Variant records, if present

Not yet inspected: the variant rows.
Next step: choose one question and query the relevant records.
Example response format, not a claim that these files were read. The paths in your response should match your folder.

If the files are missing

  • If Codex lists an empty folder, check the selected project and the location where you extracted the download.
  • If it sees only an archive, extract that archive and ask it to inspect the resulting folder.
  • If a file cannot be read, ask for the exact path and error. Follow the bundle’s usage instructions before installing a reader or querying binary tables.
  • Having files on your computer does not mean model processing stays on your computer. Use the synthetic exercise in the next lesson if you want to practice before providing personal data.

Before you continue

Check each item when you can do it.

Next tutorial

Ask your first genome question

Follow a synthetic example from one question to a saved, checkable answer.