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], [0.0], [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 (float or None) – rate of active promoter switches to inactive one

  • b (float or None) – rate of inactive promoter switches to active one

  • la (float or None) – lambda_: 4sU labelling rate

  • aa (float or None) – transcription rate with active promoter

  • ai (float or None) – transcription rate with inactive promoter

  • si (float or None) – sigma, degradation rate

  • be (float or None) – beta, splicing rate

  • ga (float or None) – gamma: the fraction of labeled u turns to unlabeled s

  • C0 (numpy.ndarray (default: np.zeros((5, 1)))) – 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 of between and end time of simulation

  • n_traj – number of simulation trajectory to use

  • t_eval (float or None) – the time points at which data is simulated

  • dt (float (default: 1)) – delta t used in simulation

  • method (str (default: basic)) – method to simulate the expression dynamics

  • verbose (bool (default: False)) – whether to report running information

Returns

adata – an Annodata object containing the simulated data.

Return type

AnnData