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] (default: None)) – rate of active promoter switches to inactive one.

  • b (Optional[float] (default: None)) – rate of inactive promoter switches to active one.

  • la (Optional[float] (default: None)) – lambda_: 4sU labelling rate.

  • aa (Optional[float] (default: None)) – transcription rate with active promoter.

  • ai (Optional[float] (default: None)) – transcription rate with inactive promoter.

  • si (Optional[float] (default: None)) – sigma, degradation rate.

  • be (Optional[float] (default: None)) – beta, splicing rate.

  • ga (Optional[float] (default: None)) – gamma, the fraction of labeled u turns to unlabeled s.

  • C0 (ndarray (default: array([[0.],        [0.],        [0.],        [0.],        [0.]]))) – 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 (default: [0, 50])) – list of between and end time of simulation.

  • n_traj (int (default: 1)) – number of simulation trajectory to use.

  • t_eval (Optional[float] (default: 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.

Return type:

AnnData

Returns:

An Annodata object containing the simulated data.