Quick Start¶

This guide will help you get started with DeepCritical in just a few minutes.

1. Basic Usage¶

DeepCritical uses a simple command-line interface. The most basic way to use it is:

uv run deepresearch question="What is machine learning?"

This will run DeepCritical with default settings and provide a comprehensive analysis of your question.

2. Enabling Specific Flows¶

DeepCritical supports multiple research flows. You can enable specific flows using Hydra configuration:

# Enable PRIME flow for protein engineering
uv run deepresearch flows.prime.enabled=true question="Design a therapeutic antibody for SARS-CoV-2"

# Enable bioinformatics flow for data analysis
uv run deepresearch flows.bioinformatics.enabled=true question="What is the function of TP53 gene?"

# Enable deep search for web research
uv run deepresearch flows.deepsearch.enabled=true question="Latest advances in quantum computing"

3. Multiple Flows¶

You can enable multiple flows simultaneously:

uv run deepresearch \
  flows.prime.enabled=true \
  flows.bioinformatics.enabled=true \
  question="Analyze protein structure and function relationships"

4. Advanced Configuration¶

For more control, use configuration files:

# Use specific configuration
uv run deepresearch --config-name=config_with_modes question="Your research question"

# Custom configuration with parameters
uv run deepresearch \
  --config-name=config_with_modes \
  question="Advanced research query" \
  flows.prime.params.adaptive_replanning=true \
  flows.prime.params.manual_confirmation=false

5. Batch Processing¶

Run multiple questions in batch mode:

# Multiple questions
uv run deepresearch \
  --multirun \
  question="First question",question="Second question" \
  flows.prime.enabled=true

# Using a batch file
uv run deepresearch \
  --config-path=configs \
  --config-name=batch_config

6. Development Mode¶

For development and testing:

# Run in development mode with additional logging
uv run deepresearch \
  question="Test query" \
  hydra.verbose=true \
  flows.prime.params.debug=true

# Test specific components
make test

# Run with coverage
make test-cov

7. Output and Results¶

DeepCritical generates comprehensive outputs:

• Console Output: Real-time progress and results
• Log Files: Detailed execution logs in outputs/
• Reports: Generated reports in various formats
• Artifacts: Data files, plots, and analysis results

8. Tools¶

Tool Ecosystem¶

DeepCritical provides a rich ecosystem of specialized tools organized by functionality:

• Knowledge Query Tools: Web search, database queries, knowledge base access
• Sequence Analysis Tools: BLAST searches, multiple alignments, motif discovery
• Structure Prediction Tools: AlphaFold, homology modeling, quality assessment
• Molecular Docking Tools: Drug-target interaction analysis
• Analytics Tools: Statistical analysis, data visualization, machine learning

Using Tools¶

Tools are automatically available to agents and workflows:

# Tools are used automatically in research workflows
uv run deepresearch flows.prime.enabled=true question="Design a protein with specific binding properties"

Tool Configuration¶

Configure tool behavior in your configuration files:

# Tool-specific configuration
tool_configs:
  web_search:
    max_results: 20
    timeout: 30
  bioinformatics_tools:
    blast:
      e_value_threshold: 1e-5

10. Next Steps¶

After your first successful run:

1. Explore Flows: Try different combinations of flows for your use case
2. Customize Configuration: Modify configs/ files for your specific needs
3. Add Tools: Extend the tool registry with custom tools
4. Contribute: Join the development community

11. Getting Help¶

• Documentation: Browse this documentation site
• Issues: Report bugs or request features on GitHub
• Discussions: Join community discussions
• Examples: Check the examples directory for usage patterns

12. Troubleshooting¶

If you encounter issues:

1. Check Logs: Look in outputs/ directory for detailed error messages
2. Verify Dependencies: Ensure all dependencies are installed correctly
3. Check Configuration: Validate your Hydra configuration files
4. Update System: Make sure you have the latest version

For more detailed information, see the Configuration Guide and Architecture Overview.