UpdatePopulation¶
UpdatePopulation
This is the main class of the UPMaBoSS API, used to build the Update Population simulation from a MaBoSS simulation and an optional UPMaBoSS specific file (.upp).
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class
maboss.upp.UpdatePopulation(model, uppfile=None, previous_run=None, nodes_init=None, verbose=False)[source]¶ -
construct a simulation for Update Population MaBoSS.
Parameters: - model – MaBoSS model
- uppfile – upp file, default to None
- previous_run – previous run to start from, default to None
- nodes_init – dict in the form { “node1” : TrueProb1, “node2” : TrueProb2, …} with nodes to be initialised to a specific value at the start of the simulation. These values override the previous run probabilities for the specified nodes, default to None
- verbose – boolean to activate verbose mode, default to False
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UpdatePopulation.run(workdir=None, overwrite=None, verbose=False, host=None, port=7777, cmaboss=False, only_final_state=False)[source]¶ -
Runs the simulation
Parameters: - workdir – (optional) Working directory in which to save result files
- overwrite – (optional) Boolean to indicate if you want to overwrite existing results in the working directory
- verbose – (optional) Boolean to indicate if you want debugging information
- host – (optional) Host to use when simulating on a MaBoSS server
- port – (optional) Port to use when simulating on a MaBoSS server
Returns: The Update Population results object.
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UpdatePopulation.setDeathNode(death_node)[source]¶ -
Modifies the identifier of the node used to represent cellular death
Parameters: death_node – The identifier of the node to be used to represent death -
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UpdatePopulation.setDivisionNode(division_node)[source]¶ -
Modifies the identifier of the node used to represent cellular division
Parameters: division_node – The identifier of the node to be used to represent division -
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UpdatePopulation.setExternalVariable(name, formula, overwrite=False)[source]¶ -
Creates a rule to update the external variable at each step
Parameters: - name – The identifier of the variable to be updated
- formula – The formula for the variable’s update
- overwrite – (optional) Overwrite the rule if one already exists for the given name
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