Getting Started
Set up CATO and create your first research project in under 5 minutes.
1. Create a Project
Projects are the primary organizational unit in CATO. Each project contains your datasets, chat sessions, visualizations, and analysis history.
- From the home screen, click New Project
- Enter a project name (e.g., "NSCLC Phase IV Study")
- Optionally add a description and color-coded labels for organization
- Select a citation format (JAMA, APA, Chicago, Vancouver, etc.)
- Click Create Project
Tip: Use descriptive names that include the study phase, date range, or cohort identifier for easy reference. Labels help you filter and organize multiple projects.
Guided Tour: First-time users will see an interactive tour after creating their first project. The tour walks you through key features including data upload, folders, chat, and more.
2. Upload Your Data
Navigate to the Database tab in your project to upload datasets. CATO supports 40+ file formats across genomics, single-cell, imaging, proteomics, and more.
| Category | Formats |
|---|---|
| Tabular | CSV, TSV, Excel, Parquet, Feather, SAS, Stata, JSON |
| Genomics | FASTA, FASTQ, VCF, GFF/GTF, BED, GenBank, GMT, Newick |
| Single-Cell | H5AD (AnnData), HDF5, FCS (flow cytometry) |
| Molecular | PDB, CIF, SDF, MOL, MOL2, SMILES |
| Imaging | NIfTI (.nii, .nii.gz), DICOM (.dcm) |
| Proteomics | mzML, MGF |
| Documents | PDF, SQL, TXT, Markdown, PNG, JPG, SVG |
| Other | MATLAB, NumPy, GML, GraphML, ZIP/TAR archives |
Single File Upload
Click Upload or drag & drop files. Max size varies by subscription tier (25MB-Unlimited).
Batch Upload
Upload ZIP/TAR archives with multiple files. Each file is imported as a separate dataset.
Folder Organization
Create nested folders to organize datasets by type, phase, or analysis.
3. Start a Chat Session
Open the Chat tab to interact with CATO's multi-agent AI system.
Multi-Agent AI Architecture
CATO uses a tiered AI system with a central orchestrator and specialized subagents. The capability level depends on your selected AI tier:
- Lite — Fast orchestrator + standard coder (budget-friendly)
- Pro — Balanced orchestrator + balanced coder (recommended)
- Ultra — Most capable orchestrator + most capable coder (maximum quality)
Specialized subagents handle domain-specific tasks:
- Coder Agent — Complex code generation & statistical analysis
- Reader Agent — Fast multi-file data exploration
- Researcher Agent — Literature search (PubMed, BioRxiv)
- Analyzer Agent — Deep exploratory data analysis
What You Can Do:
- Ask questions about your data in natural language
- Reference datasets with @mentions for precision
- Generate publication-quality visualizations (30+ chart types)
- Perform statistical analyses (t-tests, ANOVA, regression, survival analysis)
- Use / slash commands for quick actions (/profile, /visualize, /clean, /test, /code, /export)
- Toggle Plan mode with Shift+Tab for step-by-step analysis planning
- Access 200+ biomedical tools (gene lookup, pathways, drug interactions)
- Search literature (PubMed, BioRxiv, MedRxiv) with automatic citations
- Export results as CSV, Excel, DOCX reports, or PowerPoint presentations
- Edit and annotate figures with the Figure Editor (pencil icon, Base+ plans)
- View interactive 3D molecular structures (PDB, SDF, MOL2, CIF, XYZ)
- Share conversations with collaborators via public read-only links
- Use Literature Intelligence for multi-source academic search, evidence extraction, citation networks, and AI document generation
4. Navigate the Interface
The CATO interface consists of these main areas:
Left Sidebar
Navigate between projects (pinned, recent, all), filter by labels, manage project settings
Top Header
Search projects (⌘K), user menu, settings, billing, help resources
Project Tabs
Switch between Database (datasets & folders), Chat (AI assistant), and Literature (academic search & analysis)
Chat Sidebar
Conversation history, new chat sessions, memory settings
Main Panel
Chat messages with streaming responses, visualizations, code blocks, file artifacts
Visualizations Panel
Gallery of all generated charts with download options (opens automatically)
5. Learn Key Shortcuts
Speed up your workflow with keyboard shortcuts:
| Shortcut | Action |
|---|---|
| ⌘ K | Open command palette / search projects |
| Shift Tab | Toggle Plan mode in chat |
| / | Open slash commands menu |
| @ | Mention a dataset in chat |
| ⌘ N | New chat session |
6. Understand Your Plan
CATO offers five subscription tiers with different limits. Each tier includes a monthly AI budget measured in dollars — your usage is displayed as a percentage in Settings → Billing:
| Plan | Projects | AI Budget/Month | Price |
|---|---|---|---|
| Free | Unlimited | $3 | $0 |
| Base | Unlimited | $15 | $25/mo |
| Pro | Unlimited | $80 | $100/mo |
| Pay-as-you-go | Unlimited | Unlimited | Per-usage |
| Enterprise | Unlimited | Unlimited | Custom |
View your current usage and upgrade options in Settings → Billing.
Note: Some features are tier-restricted: the Figure Editor and 3D Molecular Viewer require Base or above, and Systematic Review requires Pro or above. When you exceed your monthly AI budget, chat and literature features will be temporarily blocked until the next billing cycle or until you upgrade.
Next Steps
- Data Management →Learn about all file formats and folder organization
- CATO Chat →Master @-mentions, slash commands, plan mode, and biomedical tools
- Literature Intelligence →Search PubMed, BioRxiv, arXiv, and more with evidence extraction and citation networks
- Keyboard Shortcuts →Complete reference for all keyboard commands
- Best Practices →Recommended workflows for effective research