Protocols

Protocols control what happens to the cell(s) throughout the simulation. There are currently 3 types of protocols:

1. Current Clamp: stimulates the cell at a given frequency

2. Voltage Clamp: fixes the transmembrane voltage for specific lengths of time

3. Grid: for 1D fiber, and 2D grid simulations stimulating as in Current Clamp

class PyLongQt.Protocols.ClampView

Interface for voltages clamps. Access through clamps in Voltage Clamp Protocol

__delitem__(self: PyLongQt._PyLongQt.Protocols.ClampView, index: int) → None

Delete a clamp from the list of clamps

index

That clamp’s index in the ordered list of clamps

__getitem__(self: PyLongQt._PyLongQt.Protocols.ClampView, index: int) → Tuple[float, float]

Retrieves the clamps start time (ms) and voltage (mV)

index

That clamp’s index in the ordered list of clamps

__iter__(self: PyLongQt._PyLongQt.Protocols.ClampView) → iterator

Iterate over clamps

fromList(self: PyLongQt._PyLongQt.Protocols.ClampView, voltageList: List[Tuple[float, float]]) → None

Import clamps from a list

insert(*args, **kwargs)

Overloaded function.

1. insert(self: PyLongQt._PyLongQt.Protocols.ClampView, pair: Tuple[float, float]) -> int

Insert a new clamp into the list of clamps

pair

The clamp’s start time (ms) and voltage (mV)

2. insert(self: PyLongQt._PyLongQt.Protocols.ClampView, time: float, voltage: float) -> None

Insert a new clamp into the list of clamps

time

The clamp’s start time (ms)

voltage

The clamp’s voltage (mV)

setVoltage(self: PyLongQt._PyLongQt.Protocols.ClampView, index: int, voltage: float) → None

Change the voltage of a clamp

index

That clamp’s index in the ordered list of clamps

voltage

The clamp’s voltage (mV)

class PyLongQt.Protocols.CurrentClamp

property bcl

The basic cycle length (ms). After stimt the cell will be stimulated every bcl miliseconds.

property numstims

The total number of times the stimulus should be applied in the simulation

property paceflag

If the cell should be stimulated. When this is falce no other stimulus related parameters have an effect

property stimdur

The duration of each stimulus (ms)

property stimt

The time (ms) at which the first stimulus should be applied

property stimval

The current at which the cell should be stimulated

class PyLongQt.Protocols.GridProtocol

This protocol is for 1D fibers or 2D grids of cells. It allows for current clamp like” “simulations with the groups of cells rather than just individual cells as in Voltage Clamp and” “Current Clamp.

property grid

The structure of cells, if this is 1D then it is a fibre simulation, if it’s 2D then it’s a grid simulation.

property stimNodes

The cells which the current stimulus will be applied to. The cells not on this list will not be excited directly but may excited by their neighbors.

class PyLongQt.Protocols.ParsVeiw

Interface for working with Protocol variables. Accessable through pars property in each Protocol.

__contains__(self: PyLongQt._PyLongQt.Protocols.ParsVeiw, name: str) → bool

Checks if the protocol has that parameter

name

The name of the parameter

__getitem__(self: PyLongQt._PyLongQt.Protocols.ParsVeiw, name: str) → str

Retrieves the parameter’s value

name

The name of the parameter

__iter__(self: PyLongQt._PyLongQt.Protocols.ParsVeiw) → iterator

Iterate over parameters

__setitem__(self: PyLongQt._PyLongQt.Protocols.ParsVeiw, name: str, value: str) → None

Sets the parameter to value

name

The name of the parameter

value

The new value

getType(self: PyLongQt._PyLongQt.Protocols.ParsVeiw, name: str) → str

Retrieves the parameter’s class type

name

The name of the parameter

class PyLongQt.Protocols.Protocol

The base class of all protocols

property cell

The cell model used in the simulation

cellOptions(self: PyLongQt._PyLongQt.Protocols.Protocol) → List[str]

The names of the cell models which this protocol can take

property cellStateDir

The directory to read/write the complete state of the cell model. .. Note: this is an expiremental feature and may not work correctly for every cell

property cellStateFile

The file name to of the cell state. See cellStateDir.

clone(self: PyLongQt._PyLongQt.Protocols.Protocol) → PyLongQt._PyLongQt.Protocols.Protocol

Create a copy/clone of the protocol

property datadir

The directory where the results of the simulations will be saved.

property firstRun

Time to start running runDurring

property meastime

The time (ms) when the measure manager will begin measuring.

property measureMgr

The manager for cell’s measured variables. Many of the cell model’s internal variables can be tracked throughout the simulation and functions of those variables can be recored, such as the peak, min, etc. The advantage to using this interface rather than computing these measures post simulation is that within LongQt they can be computed using every time step, while usually only a fraction of the timesteps are saved. This reduces the amount of disk space and computational time needed.

mkDirs(self: PyLongQt._PyLongQt.Protocols.Protocol) → None

Create datadir (will be called automatically when simulations are run)

property numruns

Number of times to run runDurring

property numtrials

The totoal number of trials (simulations) to be run.

property pars

property pvars

The cell’s properties. These are cell model constants which are not changed throughout the simulation, but may be different from one trial (simulation) to annother

property readCellState

Whether the cell state should be read

property runEvery

Frequency to run runDurring

runSim(self: PyLongQt._PyLongQt.Protocols.Protocol) → bool

Run all the trials consecutively.

runTrial(self: PyLongQt._PyLongQt.Protocols.Protocol) → bool

Run the current trial

setCellByName(self: PyLongQt._PyLongQt.Protocols.Protocol, cellName: str) → bool

Set the cell using its name rather than a cell model object

name

The name of the cell model

setDataDir(self: PyLongQt._PyLongQt.Protocols.Protocol, name: str = '/data', basedir: str = '', appendtxt: str = '', append_date: bool = True) → None

Set the directory where the results of the simulations will be saved.

datadir = basedir + name + datetime + appendtxt + (optional number for uniqueness) :name: the name of the datadir, if this is omitted the standard naming scheme will be used :basedir: the directory where the datadir will be created, if omited basedir will be used (the basedir property will be set) :appendtxt: additional text to be appended to the end :append_date: if datetime will be appended after name

setRunAfter(self: PyLongQt._PyLongQt.Protocols.Protocol, func: Callable[[PyLongQt._PyLongQt.Protocols.Protocol], None]) → None

This takes a function which will be called after the simulation is finished. The function must take a the protocol class which will be run as an arguement, and it should not return anything.

setRunBefore(self: PyLongQt._PyLongQt.Protocols.Protocol, func: Callable[[PyLongQt._PyLongQt.Protocols.Protocol], None]) → None

This takes a function which will be called before the simulation is started but after the simulation has been setup. The function must take a the protocol class which will be run as an arguement, and it should not return anything.

setRunDuring(self: PyLongQt._PyLongQt.Protocols.Protocol, func: Callable[[PyLongQt._PyLongQt.Protocols.Protocol], None], firstRun: float = -1, runEvery: float = -1, numruns: int = -1) → None

This takes a function which will be called durring the simulation at time firstRun, and then every runEvery after that until the end of the simulation or func has been run numruns number of times.The function must take a the protocol class which will be run as an arguement, and it should not return anything.

property simvarfile

The file where the simulation settings will be written. The settings include the protocol configuration, the cell, the cell’s properties, the measures, as well as the structure: in short almost everything. The directory will be datadir.

property tMax

The maxium length of each simulation (ms)

property trial

The current trial number. Different trials with have cell parameters. See pvars for more detial.

property type

The name of the protocol class

property writeCellState

Whether the cell state should be written

property writeint

How often the cell’s variable traces should be recored. Every writeint number of simulation timesteps the traces will be recorded.

property writetime

The time (ms) when traces will begin being recorded

class PyLongQt.Protocols.VoltageClamp

This protocol fixes the cell model’s transmembrane voltage to different values throughout the course of the simulation as defined by the clamp list

property clamps

The list of clamps which fix the cells transmembrane voltage to a specfic value (mv) starting at a time (ms). The pairs in the list are (time, voltage), and are ordered by time.