- 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
float]) – rate of active promoter switches to inactive one
float]) – rate of inactive promoter switches to active one
float]) – transcription rate with active promoter
float]) – transcription rate with inactive promoter
float]) – gamma, the fraction of labeled u turns to unlabeled s
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.
List) – list of between and end time of simulation
int) – number of simulation trajectory to use
float]) – the time points at which data is simulated
float) – delta t used in simulation
str) – method to simulate the expression dynamics
bool) – whether to report running information
an Annodata object containing the simulated data.
- Return type: