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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