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).

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

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.

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

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

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

UpdatePopulation.setStepNumber(step_number)[source]
Modifies the number of step of the simulation
Parameters:

step_number – The number of steps of the simulation