neurorosettes.clocks#

This module deals with the proliferation, differentiation and death cycles

Module Contents#

Classes#

Clock

Class to represent a cell's internal clock.

CellClocks

Class to represent all of the internal biological clocks of a cell.

ClocksFactory

Helper class to create instances of cell internal clocks based on the same rates.
class neurorosettes.clocks.Clock(rate=None)[source]#

Class to represent a cell’s internal clock.

Cells start in an inactive status and can be flagged for an event based on a rate. Alternatively, this status can be manually induced. Active states can also be blocked. When a rate is not defined, cells remain in an inactive state.

Parameters:

rate (Optional[float]) – The rate of the clock’s event

set_rate(rate)[source]#

Sets the clock’s event rate.

Parameters:

rate (float) – The clock’s event rate

Return type:

None

advance_clock(timestep)[source]#

Updates the cell cycle status based on the proliferation rate (may happen or not).

Parameters:

timestep (float) – The simulation time step (time passed between status updates).

Return type:

None

flag()[source]#

Updates the cell cycle to proliferation (will always happen)

Return type:

None

remove_flag()[source]#

Updates the cell cycle to arrest (will always happen)

Return type:

None

trigger_block()[source]#

Activates the cycle block to avoid proliferation

Return type:

None

class neurorosettes.clocks.CellClocks(proliferation_rate, death_rate, differentiation_rate)[source]#

Class to represent all of the internal biological clocks of a cell.

Parameters:

  • proliferation_rate – A cell’s proliferation rate.

  • death_rate – A cell’s death rate.

  • differentiation_rate – A cell’s differentiation rate.

set_proliferation_clock(proliferation_rate)[source]#

Sets the proliferation rate.

Parameters:

proliferation_rate (float) – A cell’s proliferation rate

set_death_clock(death_rate)[source]#

Sets the death rate.

Parameters:

death_rate (float) – A cell’s proliferation rate

set_differentiation_clock(differentiation_rate)[source]#

Sets the differentiation rate.

Parameters:

differentiation_rate (float) – A cell’s differentiation rate

set_clocks(proliferation_rate, death_rate, differentiation_rate)[source]#

Sets the rates for all biological events (proliferation, death and differentiation).

Parameters:

  • proliferation_rate (float) – A cell’s proliferation rate

  • death_rate (float) – A cell’s proliferation rate

  • differentiation_rate (float) – A cell’s differentiation rate

Return type:

None

get_clock_rates()[source]#

Returns all the clock rates for biological events.

Return type:

Tuple[float, float, float]

advance_clocks(timestep)[source]#

Advance all biological clocks and flag cells for biological events.

Parameters:

timestep (float) – The simulation time step (time passed between status updates)

block_all_clocks()[source]#

Blocks the cycling, death and differentiation clocks.

class neurorosettes.clocks.ClocksFactory[source]#

Helper class to create instances of cell internal clocks based on the same rates.

proliferation_rate: float#

The rate of proliferation of the cells.

death_rate: float#

The rate of death of the cells.

differentiation_rate: float#

The rate of differntiation of the cells.

get_clocks()[source]#

Returns an instance of a CellClocks object with the chosen biology rates.

Return type:

CellClocks