Download Simulator

Download ctRSD-simulator -> DOWNLOAD

The following packages are used internally within the simulator and will need to be installed and available in the Python environment the simulator is running within: numpy, scipy, matplotlib, re, math, xlrd

Table of Contents

Here you will be able to access information on all of the different components of the ctRSD-simlator 2.0. Please take a look at our overview to become familar with the simulator.

General:

• Overview
• Model Reactions and Implementation
  • Model overview
  • ctRSD Reaction Schematics
    • Base ctRSD Reactions
    • Fuel Reactions
    • AND Gate Reactions
    • Degradation Reactions
    • Thresholding Reactions
    • Comparator Gate Reactions
  • Detailed model description
• Installing and Initializing Simulator
• RSD_sim Class
  • Class Object
  • Initializations
• Functions
  • Quick reference
  • global_rate_constants()
  • molecular_species()
  • simulate()
  • output_concentration()
• Sequence Compiler
  • Download Domains List
  • Function Overview
  • Function Documentation
  • Examples
• Troubleshooting
  • Accessing Variables in the Simulator
  • Not specifying enough domains in RSD_sim() initialization
  • Simulations taking a long time
  • Speeding Up Comparator Gate Simulations
  • Overriding Rate Constants

General Examples:

• Simple Examples
  • Single ctRSD Gate Reaction
  • Two-Layer Cascade Simulation
  • Fan-Out Simulation
  • Fan-Out Fan-In Simulation
  • Experimental Nomenclature
• Advanced Simulator Features
  • Discontinuous Simulation
  • Degradation Simulation
  • Two-Toehold Cascade Simulation
  • AND Gate with Fuel Simulation
  • Two AND Gate OR Simulation
  • Thresholding Simulation
  • Seesaw AND Element Simulations
    • ctRSD seesaw element simulation
    • DNA seesaw AND element simulation
  • Comparator Gate Simulation
  • Three Comparator Gate Simulation

Examples from Publications:

• 2022 Science Advances Paper
  • Figure 2D
  • Figure 4C
  • Figure 4F
  • Figure 4H
  • Figure 5B
  • Figure 5C
  • Figure 5D
  • Figure 5E
  • Figure 5F
  • SI Figure 12
  • SI Figure 16
  • SI Figure 18
  • SI Figure 19
  • SI Figure 26
  • SI Figure 27B
  • SI Figure 30C
  • SI Figure 31B
• 2023 ACS Synthetic Biology Paper