resim package¶
Subpackages¶
Submodules¶
resim.command_line module¶
ReSim - entry point
-
resim.command_line.
run_resim_flask
()¶ run resim flask from command prompt
resim.core module¶
ReSim: chemoREsistance SIMulator
ReSim (chemoREsistance SIMulator) simulates cancer chemoresistance dynamics based on a stochastic model. The model describes the interaction between chemotherapeutics and various cancer cell subpopulations (including sensitive, primary resistant, acquired resistant and quiescent cancer cells).
Examples
- minimal setup using default parameters:
>>> import resim >>> model = resim.Simulator() >>> res = model.simulate()
- set your own params:
>>> model = resim.Simulator(gr=[0.02, 0.1, 0.1])
- or
>>> model = resim.Simulator() >>> model.set_param_gr([0.02, 0.1, 0.1])
- or
>>> model = resim.Simulator() >>> model.gr_s = 0.02 >>> model.gr_pr = 0.1
Please set t using set_param_t instead of assign directly to model.t.
- Attribute:
- sig (int): calibrated diffusion constant for the set of stochastic differential equations. ccmax (float): tumor carrying capacity (10^8).
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class
resim.core.
Simulator
(gr=[0.015, 0.015, 0.015], k=[1e-06, 0.0001, 0.0005, 1e-06, 0.0005, 1e-06, 0.0005, 0.0005, 0.0005, 0.0005], d=[10, 10, 240, 0.9, 0.7], init=[0.42, 0.05, 0, 0.03, 0], t=365, n=50)¶ ReSim Simulator Class
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set_param_d
(d)¶ Set drug related parameters
Parameters: d (list of floats) – drug related constants (ki, qf, dose, dsmax, ke).
Raises: ValueError
– if d length not equal to 5.ValueError
– if any elements in d smaller than 0.
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set_param_gr
(gr)¶ Set growth rates
Parameters: gr (list of floats) – growth rate of cancer cells (gr_s, gr_pr, gr_ar).
Raises: ValueError
– if gr length not equal to 3.ValueError
– if any elements in gr smaller than 0.
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set_param_k
(k)¶ Set k
Parameters: k (list of floats) – kinetic constants (ks_pr, ks_ar, ks_q, kpr_s, kpr_q, kar_s, kar_q, kq_s, kq_pr, kq_ar).
Raises: ValueError
– if k length not equal to 10.ValueError
– if any elements in k smaller than 0.
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set_param_t
(t)¶ Set t
set self.t (int) and self._tspan (numpy array).
Parameters: t (int) – simulation time frame in days e.g. 365d = 1y. Raises: ValueError
– if t is smaller than 0.
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simulate
()¶ Simulate based on Simulator attributes
Returns: dict of dictionaries with keys ‘control’ and ‘case’. Both ‘control’ and ‘case’ holds a dictionary of pandas data frame with keys ‘cells’, ‘drugs’ and ‘fht’. Return type: dict
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resim.plot module¶
ReSim - Plotting Module
Visualize resim result.
Examples
- Available functions:
>>> snsplt_cells = resim.plot_cells(res) >>> snsplt_drug = resim.plot_drug(res) >>> snsplt_fht = resim.plot_fht(res)
- You may save the plots in png.
>>> snsplt_cells.figure.savefig('resim_cells.png') >>> snsplt_drug.figure.savefig('resim_drug.png') >>> snsplt_fht.figure.savefig('resim_fht.png')
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resim.plot.
plot_cells
(res, subplot=False)¶ Plot cells
Parameters: - res (dict) – dict return by .simulate().
- subplot (bool) – Default is False. True to plot different type of cells
- different plot. (in) –
Returns: seaborn plot object
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resim.plot.
plot_drug
(res)¶ Plot Drug Dynamics
Parameters: res (dict) – dict return by .simulate(). Returns: seaborn plot object
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resim.plot.
plot_fht
(res)¶ Plot first hitting time (progression free survival)
Parameters: res (dict) – dict return by .simulate(). Returns: seaborn plot object