dynamo.sim.Gillespie
- dynamo.sim.Gillespie(a=None, b=None, la=None, aa=None, ai=None, si=None, be=None, ga=None, C0=array([[0.], [0.], [0.], [0.], [0.]]), t_span=[0, 50], n_traj=1, t_eval=None, dt=1, method='basic', verbose=False)[source]
A simulator of RNA dynamics that includes RNA bursting, transcription, metabolic labeling, splicing, transcription, RNA/protein degradation.
- Parameters:
a (
Optional
[float
]) – rate of active promoter switches to inactive one.b (
Optional
[float
]) – rate of inactive promoter switches to active one.aa (
Optional
[float
]) – transcription rate with active promoter.ai (
Optional
[float
]) – transcription rate with inactive promoter.ga (
Optional
[float
]) – gamma, the fraction of labeled u turns to unlabeled s.C0 (
ndarray
) – A numpy array with dimension of 5 x n_gene. Here 5 corresponds to the five species (s - promoter state, ul, uu, sl, su) for each gene.t_span (
List
) – list of between and end time of simulation.n_traj (
int
) – number of simulation trajectory to use.t_eval (
Optional
[float
]) – the time points at which data is simulated.dt (
float
) – delta t used in simulation.method (
str
) – method to simulate the expression dynamics.verbose (
bool
) – whether to report running information.
- Return type:
- Returns:
An Annodata object containing the simulated data.