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Simulation Tools: CFS & C6

This page explains how to simulate DNA construction workflows using two tools: - CFS (Construction File Simulator) — a Java-based simulation engine. - C6 Tools — a spreadsheet-based interface using Google Sheets.

🧪 CFS (Construction File Simulator)

CFS is a Java tool that simulates a Construction File (CF) to verify correctness of molecular biology protocols like PCR, digestion, ligation, assembly, and transformation. It detects common design issues before you build.

Getting Started

  1. Install Java (JRE 8+).
  2. Download the .jar file from the Releases section.
  3. Extract dist.zip, if applicable.

Usage Options

  • Double-click ConstructionFileSimulator.jar to launch the GUI.
  • Drag-and-drop an experiment folder onto the GUI.
  • Command line (GUI launch): 
    java -jar ConstructionFileSimulator.jar
  • Command line (direct simulation): 
    java -jar ConstructionFileSimulator.jar /path/to/experiment/folder

File Requirements

A valid experiment folder must include: - A text-based Construction File - GenBank files for sequence definitions - A TSV file with part definitions (if needed)

Output

The simulator will display: - Each intermediate step (e.g., PCR product, digested fragment) - Final output sequences - Errors or misassemblies if present

📊 C6 Tools (Spreadsheet-based)

C6 Tools is a Google Sheets-based simulation interface using built-in scripts.

Example Layout

You define steps as a grid:

A B C D E F
PCR P6libF P6libR pTP1 3583 P6
Assemble P6 BsaI pP6
Transform pP6 Mach1 Carb

Supporting rows include definitions of primers and templates below.

How to Use

  1. Fill in your construction steps as a grid (A6:F12 in this example).
  2. Run this in a new cell to parse: 
    =parseCF(A7:F12)
  3. Simulate the build using: 
    =simCF(H8)

Output

The simulation will populate: - Intermediate products - Final product - Sequence output or errors

Use these tools to validate and troubleshoot your designs before going to the bench. They are critical for catching errors early and speeding up the design-build-test cycle.