MIT Principles of Synthetic Biology Term Project: Modeling in vivo strand displacement cascades to identify regimes of digital logic robustness to rates of RNA production and degradation.
analyze_system.py -- a few examples showing how to cycle through inputs to AND/OR/NOT and record the output levels after a certain amount of time in a convenient table.
Gates.py -- classes defining the AND, OR, NOT, INP, REP components
helpers.py -- a few helper functions used here and there
main.py -- the main System class is defined here for now. Has examples of how to define AND/OR/NOT systems
Strands.py -- classes defining the strand-based components (SignalStrand, GateStrand, GO/Gate-Output complex, DynamicGate, Th/Threshold, Reporter
sys_AND.py -- the output code of the AND system, allows one to analyze an AND gate
sys_NOT.py -- similar for the NOT gate
sys_OR.py -- similar for the OR gate