phylovelo.gillespie_variable_paras
Classes
Cell class |
|
Cell division/differentiation type |
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Gillespie simulation |
Module Contents
- class Cell(Ngene: int = None, state: int = 0, gen: int = None, cid: int = None, parent: int = None, tb: float = None, td: float = None)
Cell class
- Args:
- Ngene:
Gene number
- state:
Cell type
- gen:
Cell generation
- cid:
Cell id
- parent:
Cell’s parent
- tb:
Birth time
- td:
Death time
- state = 0
- parent = None
- cid = None
- gen = None
- tb = None
- td = None
- class Reaction(rate: callable = None, num_lefts: list = None, num_rights: list = None, index: int = None)
Cell division/differentiation type
- Args:
- rate:
reaction rate function
- num_lefts:
Cell numbers before reaction
- num_right:
Cell numbers after reaction
- index:
Reaction index
- rate = None
- num_lefts
- num_rights
- num_diff
- index = None
- combine(n, s)
- propensity(n, t)
- class Gillespie(num_elements: int, inits: list = None, max_cell_num: int = 20000)
Gillespie simulation
- Args:
- num_elements:
Cell type number
- inits:
Initial cell number
- max_cell_num:
Maximum cell number
- num_elements
- reactions = []
- anc_cells = []
- curr_cells
- generation_time = [0]
- max_cell_num = 20000
- add_reaction(rate: callable = None, num_lefts: list = None, num_rights: list = None, index: int = None)
Add reactions to simulation
- Args:
- rate:
reaction rate function
- num_lefts:
Cell numbers before reaction
- num_right:
Cell numbers after reaction
- index:
Reaction index
- evolute(steps: int)
Run simulation
- Args:
- steps:
How many steps to evolute before step