FRETnet

Quickstart

Currently sim_network.py and sim_network_nogui.py simulate a 2-input AND gate. They can be run with the syntax:

python -i sim_network.py <X1> <X2>

or

python -i sim_network_nogui.py <X1> <X2>

where <X1> and <X2> are either ON or OFF.

sim_network.py prints out the activation of the output node every minute. sim_network_nogui.py prints out the activation of the output node every 10000 steps.

GUI controls

• <Enter>: advance the simulation 1 step
• <Space>: start/stop continuous simulation mode
• <Left>: slow down continuous simulation
• <Right>: speed up continuous simulation

While in GUI mode, each node is displayed with its activation (time-averaged flux) shown.

FRETnet components

utils.py

Node objects define individual fluorophores. Each Node has a decay_rate and emit_rate describing its intrinsic non-radiative decay and radiative emission rate constants, respectively (note that activation values do not distinguish between these two decay pathways). The InputNode object inherits from Node, and has an additional production_rate parameter describing its excitation rate constant via external power source. Two Nodes n1 and n2 may be linked in an input-output relationship via n2.add_input(n1)

A Network object simulations a collection of nodes. Note that for GUI simulations, the Network object need not be explicitly generated (it is created by the GUI). Each Network object collects statistics on its nodes' behavior, as well as the global simulation time.

For Network network, the simulation time is in network._time. Reaction statistics are stored in a dict (network._stats). network._stats has tuple keys following the form (rxn_type, input, output):

• rxn_type: the type of reaction (emit, decay, production, transfer, or the wildcard '*')
• input: the input node (a Node object, None, or the wildcard '*')
• output: the output node (a Node object, None, or the wildcard '*')

The value of each dict entry is a positive integer representing the number of times the reaction occurred over the course of the simulation.

The time each Node spends in each state is stored in a dict (network._node_stats), whose keys are the corresponding Node objects. The value of each dict entry is a dict mapping status (currently only 'ON' or 'OFF') to the simulation time spent in that state.

gui.py

The Simulator object generates a Tkinter window that simulates a given collection of nodes with display positions specified. See sim_network.py for example usage.