Core Workflow

1. Create one project per study.
2. Add your data in Files.
3. Check columns, warnings, units, and identifiers.
4. Say which files, versions, or papers to use.
5. Ask in Chat; ask for a plan first for important methods.
6. Follow the run in Chat and the Shell view.
7. Check files, figures, code, citations, and provenance in the Workspace.

Chat Modes

/standard · /profile · /feedback

Prompt Template

• Objective: the question or decision
• Evidence: @files and exact versions
• Population: subset and exclusions
• Method: model and assumption checks
• Outputs: files, figures, notebook, report
• When to stop: when CATO must stop and ask

Keyboard

Workspace

• Files: browse, preview, edit, upload
• Figures: viewers, SVG editing, comments, download
• Notebooks: Python/R code, output, downloads
• Manuscripts: Markdown/LaTeX, preview, Word and PDF export
• Shell: each command, its output, and a Stop button
• Memory: CATO's notes on the project
• Readers: PDF/HTML/transcript comments
• Review: what Double-check this answer found
• Provenance: how each version was made

Data and Uploads

Common types:

Tables/statistics; PDF/JSON/code; images; HDF5; genomics; single-cell; molecular; medical imaging; proteomics; graph, MATLAB, and NumPy data; ZIP/TAR archives.

No size limit on a single file, on any plan.

Archives: 500 MB, or 2 GB once extracted.

Literature

• Deep Search takes a research question and returns up to 100 papers.
• For ClinicalTrials.gov and patents, ask in Chat.
• Save papers to the Library, sort them into collections, and set up watches under Alerts.
• Open available full text in the Workspace; otherwise CATO has only the abstract.
• Send selected papers to Chat.
• Check every citation and claim against the paper.

Memory

• Project notes: in the Memory tab, shared with the project
• Your notes: in Settings → Memory, only you can see them
• Read, edit, or delete any note.
• Notes are reminders, not evidence.

If a Run Appears Stuck

1. Reopen the same conversation and let it reconnect.
2. Check the status line and the Shell view.
3. Press Stop once if you no longer want the work.
4. Check your usage in Settings → Billing.
5. Ask again only once nothing is still running.
6. Send support a link, the time, and the error, not data or passwords.

Validation Checklist

• The right files and versions
• Expected rows, variables, units, and exclusions
• Code, packages, and seed
• Assumptions, diagnostics, uncertainty, sensitivity
• Figure data, labels, scales, and accessibility
• The right paper, and that it supports the claim
• The downloaded file, and a clean re-run