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Getting Started with BoCoFlow

This guide will help you install BoCoFlow and create your first workflow.

System Requirements​

  • Operating System:
    • macOS 10.15+ (Catalina or later)
    • Linux: Ubuntu 22.04+ or compatible distributions
    • Windows 10/11 (64-bit)
  • RAM: 4GB minimum, 8GB recommended
  • Disk Space: 500MB for the application, plus space for your workflows and data
  • Python: 3.9+ (can be automatically managed by the application)

Download and Install​

1. Download the Application​

Download the latest BoCoFlow release for your platform from the official website:

  • macOS: DMG installer (universal binary for Intel and Apple Silicon)
  • Linux: AppImage (portable, works on most distributions)
  • Windows: NSIS installer (.exe)

2. Install BoCoFlow​

macOS​

  1. Open the downloaded .dmg file
  2. Drag BoCoFlow to your Applications folder
  3. Launch BoCoFlow from Applications or Spotlight

Linux​

  1. Make the AppImage executable: 
    chmod +x BoCoFlow-*.AppImage
  2. Run the AppImage: 
    ./BoCoFlow-*.AppImage

Windows​

  1. Run the downloaded .exe installer
  2. Follow the setup wizard instructions
  3. Launch BoCoFlow from the Start Menu or Desktop shortcut

3. First Launch Setup​

When you first launch BoCoFlow:

  1. Backend Installation Window appears showing installation progress
  2. Python Environment is automatically set up and configured
  3. Dependencies are installed (this takes 2-5 minutes)
  4. Main Application launches when setup completes
tip

BoCoFlow automatically manages Python environments and dependencies behind the scenes, ensuring everything is properly isolated and configured.

Creating Your First Workflow​

Step 0: Watch a Demo​

🧬 BoCoFlow Pre-release Quick Demo: A Simple Protein Simulation Workflow

Watch this step-by-step demonstration of building a computational biology workflow using BoCoFlow's drag-and-drop interface. No coding required!

🔬 Workflow Pipeline Demonstrated:

  • ✅ ESMFolding - AI-powered protein structure prediction
  • ✅ PDB2PQR - Structure processing and charge assignment
  • ✅ OpenMM - Molecular dynamics simulation setup and execution

🚀 What You'll Learn:

  • How to create visual workflows by connecting computational nodes
  • Setting up protein folding predictions with state-of-the-art ESMFold
  • Processing structures for MD simulations using PDB2PQR
  • Configuring and running molecular dynamics with OpenMM
  • Managing complex computational pipelines without writing code

Step 1: Project Setup​

  1. Launch BoCoFlow and click the Setup button in the top toolbar
  2. In the New Workflow tab, configure:
    • Working Directory: Where your workflow files will be stored
    • Database Type: Select SQLite (recommended for beginners)
    • Log Level: Choose Error for production, Verbose for debugging
  3. Click Create Workflow to initialize your workspace

Step 2: Add and Connect Nodes​

  1. Browse Available Nodes:

    • Explore the Node Menu on the left sidebar
    • Nodes are organized by category
    • Use the search bar to find specific nodes

  2. Add Nodes to Canvas:

    • Drag nodes from the sidebar onto the canvas
    • Position them to visualize your workflow

  3. Connect Nodes:

    • Click and drag from an output port (right side of node)
    • Connect to an input port (left side of another node)
    • Connections show data flow between nodes

  4. Configure Nodes:

    • Click the ⚙️ (gear) icon on any node
    • Fill in required parameters
    • Save configuration

Step 3: Execute Your Workflow​

  1. Click the Execute button in the toolbar
  2. Monitor progress in the log panel at the bottom
  3. Node colors indicate status:
    • Red: Unconfigured or failed
    • Yellow: Configured but not executed
    • Green: Successfully executed

Step 4: View Results​

  • Click the 📊 (chart) icon on any completed node to view its output
  • Results are automatically cached for future use
  • Export results using the appropriate output nodes

Understanding the Interface​

Main Components​

Toolbar (Top)

  • Setup: Configure workspace and environment settings
  • Save: Save your current workflow
  • Clear: Clear the canvas
  • Execute: Run the workflow
  • Search: Find nodes by ID

Node Menu (Left Sidebar)

  • Organized by categories
  • Searchable list of all available nodes
  • Drag nodes to canvas to use them

Canvas (Center)

  • Visual workspace for building workflows
  • Zoom and pan controls in top-right corner
  • Right-click for context menu options

Log Panel (Bottom)

  • Real-time execution logs
  • Error messages and debugging information
  • Success confirmations for completed nodes

Node States​

Nodes change color to indicate their status:

  • 🔴 Red: Not configured or execution failed
  • 🟡 Yellow: Configured and ready to execute
  • 🟢 Green: Successfully executedhelp

Environment Locations​

BoCoFlow stores its Python environments and data in platform-specific locations:

Application Data:

  • macOS: ~/Library/Application Support/bocoflow-electron/
  • Linux: ~/.config/bocoflow-electron/
  • Windows: %APPDATA%\bocoflow-electron\

Troubleshooting​

Backend Installation Issues​

If the backend installation fails on first launch:

  1. Check Internet Connection: Installation requires downloading Python packages
  2. Reset Backend: Go to Settings → Reset Backend Environment
  3. Antivirus Software: May need to add BoCoFlow to exceptions
  4. View Logs: Help → Toggle Developer Tools for detailed error messages

Port Conflicts​

If you see errors about ports 18000 or 18001 being in use:

# macOS/Linux - Find processes using ports
lsof -i :18000
lsof -i :18001

# Windows - Find processes using ports
netstat -ano | findstr :18000
netstat -ano | findstr :18001

Kill the conflicting processes or restart your computer.

Python Environment Reset​

To completely reset the Python environment:

  1. Close BoCoFlow completely
  2. Delete the environment folder (see Environment Locations above)
  3. Restart BoCoFlow to trigger a fresh installation

Next Steps​

Now that you have BoCoFlow running:

Getting Help​