pyMaBoSS

A python interface for the MaBoSS software

Here we show how to reproduce the step shown in the MaBoSS tutorial.

import maboss
import ginsim

Loading/Building the Simulation object

The file tuto.zginml can be converted in MaBoSS format by GINsim. This will produce two files, tuto.bnd and tuto.bnd.cfg.

To quickly write the script below, go to MaBoSS -> load file (zginml format).

lrg = ginsim.load("tuto.zginml")
master_simulation = ginsim.to_maboss(lrg)

Alternatively, you could also build the Simulation object from scratch by describing every node of the network.

from maboss import Node, Network
from maboss import Simulation

nd_dnaDam = Node('DNAdam', '!p53_b1 & DNAdam', 1, 1)
nd_p53_b1 = Node('p53_b1', '!p53_b2 & !Mdm2nuc | p53_b2', 1, 1)
nd_p53_b2 = Node('p53_b2', 'p53_b1 & !Mdm2nuc', 1, 1)
nd_mdm2cyt = Node('Mdm2cyt', 'p53_b1 & p53_b2', 1, 1)
nd_mdm2nuc = Node('Mdm2nuc', '!p53_b1 & !Mdm2cyt & !DNAdam | !p53_b1 & Mdm2cyt| p53_b1 & Mdm2cyt', 1, 1)

testNet = Network([nd_dnaDam, nd_p53_b1, nd_p53_b2, nd_mdm2cyt, nd_mdm2nuc])

testNet.set_istate(['p53_b1', 'p53_b2'],
                   {(0, 0): 1, (1, 0): 0, (1, 1): 0})
testNet.set_istate('Mdm2cyt', [1, 0])
testNet.set_istate('Mdm2nuc', [1, 0])
testNet.set_istate('DNAdam', [0.4, 0.6])

byHand_sim = Simulation(testNet)

By default, (if the network was built from scratch or if the .cfg file did not contain the information for a given node), all nodes have the attribute is_internal set to False. This can be changed within the script

master_simulation.network['DNAdam'].is_internal = True

You can also use a widget to produce the same effect: go to MaBoSS -> Simulation -> set output and select all the nodes that will not be internal (i.e. that are output nodes).

#maboss.wg_set_output(master_simulation)
maboss.set_output(master_simulation, ["p53_b1", "p53_b2", "Mdm2cyt", "Mdm2nuc"])

You can change other parameters with the function update_parameters:

master_simulation.update_parameters(time_tick=0.1, max_time=4)

Once all the parameters are set, you can run the simulation. The following line will create two temporary files that contains everything MaBoSS needs to know to run properly. The result of the simulation are stored in a Result object.

To run the simulation, use the command below. This command can be quickly written by going to MaBoSS -> Simulation -> run.

master_results = master_simulation.run()

To visualize the simulation, you can use the make_trajectory method of the results object.

master_results.plot_trajectory()

master_results.plot_piechart()

Handeling mutation

To mutate a gene you can call the method mutate of a simulation object. It takes as argument the name of a node and a string that can be either “ON” or “OFF”.

You can also use the widgets to produce mutants.

#mutant_simulation = maboss.wg_make_mutant(master_simulation)
mutant_simulation = maboss.copy_and_mutate(master_simulation, ["Mdm2nuc"], "ON")

mutant_res = mutant_simulation.run()

mutant_res.plot_piechart()