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Index

What can #-CAD do?

#-CAD is meant as the one-stop solution for designing and optimizing a DNA megastructure design. The key features include:

  • Visual Design: An intuitive 2D grid interface for designing megastructure slat layouts and handle binding positions
  • Handle Optimization: Evolutionary algorithm for optimizing assembly handle sequences to minimize parasitic interactions
  • 3D Visualization: Real-time 3D rendering of your designs
  • Echo Export: Direct export to Echo Liquid Handler command sheets
  • Python Integration: Seamless integration with the crisscross-kit Python library

Quick Guide

The Main Interface

The user interface is divided into three zones:

  1. 2D Grid View (left): The primary design canvas where you place and edit slats, handles and cargo tags
  2. 3D View (right): 3D visualization of design. This can be interacted with independently of the 2D grid, but edits cannot be made to the actual design from this panel.
  3. Sidebar (far-left): Context-sensitive panels that provide tools for adding, modifying or deleting slats, handles and cargo.

Design Modes

Several different design editing modes are available via the sidebar:

Mode Description
Slat Design Add, remove, and edit slats on the grid
Assembly Handles Assign, edit and optimize assembly handles
Cargo & Seed Place and edit cargo molecules and seed structures
Echo Config Configure Echo Liquid Handler export settings

Basic Workflow

  1. Create or load a design: Start with a new design or import an existing .xlsx file
  2. Design your slat layout: Place slats on the 2D grid to form your megastructure, taking care to ensure slats criscross on different layers
  3. Optimize assembly handles: Run the evolutionary algorithm to find optimal handle sequences
  4. Add cargo and seeds: Place functional elements on your design
  5. Export: Generate Echo commands or save your design for Python processing

Example Designs

Example designs are available for testing in our GitHub repository here.

Next Steps