CATO

Getting Started

Create a project, add your data, run an analysis, and look at what it made.

How CATO is organized: a project holds your data, papers, conversations, notes, and results. You ask for work in Chat, and open the results in the Workspace panel beside it.

1. Create a Project

  1. On the projects screen, select New Project. With no projects yet, choose a worked example or a card under Or start with your own work.
  2. Give it a name that says which study or question it is for.
  3. Add a description and labels if you like, and choose a citation format.
  4. Open the project. To run the guided tour again later, open the account menu and choose Start Tour.

Keep unrelated studies in separate projects, so that files and notes from one stay out of the other.

2. Add Your Data

Open Files and select Upload (a file or a whole folder), or pressCtrl/Cmd+U.

Common formats

CSV, TSV, Excel, Parquet, SAS, SPSS, Stata, JSON, PDF, images, HDF5, H5AD, FASTA/FASTQ, VCF, BED, PDB/CIF, DICOM, NIfTI, mzML, MATLAB, NumPy, and archives.

Before analysis

Check the file type, rows and columns, missing values, and any upload warning. A name such as baseline_labs.csv is easier to refer to than a generic one.

There is no size limit on a single file, on any plan. Archives have limits of their own. See Data Management for details.

3. Learn the Project Layout

Files

The project computer’s file browser: your data and everything analyses produce.

Chat

Your conversations with CATO.

Library

The papers you save, with tabs for Deep Search and Saved reports.

Workspace

The panel beside Chat where files, figures, notebooks, and manuscripts open.

Use Ctrl/Cmd+Kfor the command palette, Ctrl/Cmd+1for Files, and Ctrl/Cmd+2for Chat.

4. Choose a Mode

ModeBest forWhat to expect
StandardEveryday analysis, writing, and data exploration.The default.
ResearchHarder methods, multi-stage analysis, and evidence synthesis.Takes longer and uses more of your allowance.

Use the model control in the composer; /standard switches back to Standard.

5. Ask a Clear Question

Say which data CATO should use. Type @ to mention a dataset and / to see the commands. Ask for a plan first when you want to read the approach before anything runs.

“Profile @baseline_labs.csv. Report missingness and outliers, but do not impute yet.”

“Compare the primary outcome by treatment arm with effect size, 95% CI, assumption checks, and a publication-ready figure.”

“Using only the selected papers, build an evidence table and identify contradictions that need manual review.”

A good request names the question, the variables, the population or subset, the method, the checks you want, and the output. If a definition is ambiguous, ask CATO to confirm it before running code.

6. Follow Long-Running Work

CATO keeps working if you move to another conversation, reload the page, or close the tab. Come back to the same conversation to see where it got to.

  • Press Stop if the question or the data is wrong.
  • Do not send the same request again while a response is reconnecting.
  • If a response stops, reopen the conversation first. It says why, and what was finished is still there.
  • If your monthly allowance runs out, a response being written finishes and a run with more to do stops there.

7. Open and Refine the Results

Open files and figures in the Workspace, and use the file itself as the record rather than the chat message. Provenance, in a file's menu, shows how each version was made.

Files and data

Preview, edit text or code, choose a version, and use a generated table in later work.

Figures

Open interactive views, edit SVG figures, comment on them, and download them.

Notebooks and manuscripts

Read the code and output behind an analysis, or edit Markdown or LaTeX with a preview.

If an editor reports unsaved changes, save or discard them before switching versions or closing the file. Double-check this answer, under CATO's latest answer, lists claims the record of the work does not support. It does not replace checking the data, code, statistics, and citations yourself.

8. Search and Save Literature

Open Library → Deep Search, write a research question as a sentence, and save the papers you want to the Library. Deep Search returns up to 100 results and shows a preprint and its journal version as one result. From there you can fetch available full text, extract evidence, set up watches, and generate documents.

Fetched papers open in the Workspace, and you can send selected papers to Chat. Check citations and claims against the papers before you publish. See the Library and Deep Search guide.

9. Check CATO's Notes

CATO keeps notes so that a later conversation can pick up where the last one stopped. Project notes are in the project's Memory tab and are shared with everyone on the project. Notes about how you work are in Settings → Memory and only you can see them. You can read, edit, or delete any note.

Notes are reminders, not evidence. Cite the files, datasets, and figures themselves.

Plans and Usage

PlanPriceIncluded AI usage
Standard$20/monthMonthly usage allowance
Pro$100/month5x the Standard allowance, plus systematic reviews
Pay-as-you-goMeteredBilled for what you use, no monthly cap

Settings → Billing shows your plan, renewal date, and usage. Included AI usage is a monthly allowance, not a set number of messages, and it resets at the start of each billing period. Enterprise plans are arranged by agreement.

Next Steps