CATO

Data Management

Upload your data, check that it was read correctly, and keep track of what each result came from.

Upload Files

  1. Open Files and select Upload, then choose a file or a whole folder; or drop files or a folder onto the page; or press Ctrl/Cmd+U.
  2. Wait for the upload to finish before you start an analysis.
  3. Open each file and check its format, columns, preview, and any warning.
  4. Rename generic files, and add folders where they help.

A finished upload means the file was stored. It does not mean that dates, category codes, decimal separators, missing-value markers, character encoding, or units were read correctly, so check them.

Supported Formats

Tables and statistics

CSV, TSV, XLSX/XLS, Parquet, Feather, SAS7BDAT, SPSS SAV, Stata DTA

Structured and documents

JSON, PDF, SQL, TXT, Markdown, logs, Python, R, and shell scripts

Genomics and single-cell

FASTA/FA, FASTQ/FQ, VCF, GFF/GFF3, GTF, BED, GenBank, GMT, Newick, H5AD, MTX, Loom

Molecular and imaging

PDB, CIF, SDF, MOL, MOL2, SMILES, NIfTI, DICOM

Proteomics and cytometry

mzML, MGF, FCS, HDF5/H5, BIOM

Scientific and graph data

MATLAB MAT, NumPy NPY/NPZ, GML, GraphML

Images

PNG, JPEG, GIF, SVG, and WebP

Archives

ZIP, TAR, TAR.GZ/TGZ

Some formats show file details rather than a full preview. CATO can still analyze them.

File and Archive Limits

There is no size limit on a single file, on any plan.

ZIP and TAR archives can be up to 500 MB, and up to 2 GB once extracted. An archive that is damaged, password-protected, holds unsafe paths, or has too many files is refused.

Folders and Naming

A useful project structure

01_raw/
02_dictionary/
03_processed/
04_analysis/
05_figures/
06_manuscript/

Naming

  • • Use stable, descriptive names.
  • • Write dates as YYYY-MM-DD.
  • • Name the cohort or stage, never a patient.
  • • Do not overwrite source files.

Files CATO Makes

Cleaned tables, model outputs, notebooks, figures, and reports are saved in the project, next to your data.

  • Open a file from the response or from the Workspace.
  • When you reproduce a result, name the version, not only the filename.
  • Provenance, in a file's menu, shows how each version was made.
  • Check a generated table's row count, columns, and transformations before using it in the next analysis.

Versions

Files, figures, notebooks, and manuscripts keep their earlier versions. If you have unsaved edits, CATO asks you to save or discard them before you switch versions or close the tab.

Version history only records what changed inside CATO. Keep your source records, data dictionaries, and consent records wherever your institution requires.

What to Check

Tables

Rows, columns, types, missing values, duplicated keys, impossible values, category levels, and units.

Images and figures

Dimensions, orientation, labels, color accessibility, cropping, and the downloaded file.

Genomics and molecular data

Reference build, coordinate convention, identifiers, sample order, chain or model, and units.

Documents and papers

Text recognition, page order, citation details, and whether the full text was available.

Deleting

Deleting a file or project can break conversations, figures, or manuscripts that depend on it. Download what you need first, and check that nothing still relies on it. CATO asks you to confirm, but that is not a backup.

Security and Privacy

  • Upload only data you and your institution are allowed to process here.
  • Do not upload identifiable patient or other health data on a standard account, and remove direct identifiers and secrets.
  • Analyses run in isolated sandboxes, and data is encrypted in transit and at rest.
  • The Privacy Policy, and any agreement with your institution, set out how data is processed and kept.