from biodivine_aeon import * from pathlib import Path model_string = Path('buthanol_production.aeon').read_text() model = BooleanNetwork.from_aeon(model_string) model.num_vars()

assert model.num_parameters() == 0 graph = model.graph() for v in graph.variables(): print(graph.get_variable_name(v), "=", model.get_update_function(v)) assert model.get_update_function(v) is not None

stg = SymbolicAsyncGraph(model) attractors = find_attractors(stg) attractors

sporulation_on = stg.fix_variable("sporulation", True) on_in_attractor = attractors[0].intersect(sporulation_on).vertices().cardinality() off_in_attractor = attractors[0].minus(sporulation_on).vertices().cardinality() print("Sporulation is ON in", on_in_attractor, "states.") print("Sporulation is OFF in", off_in_attractor, "states.") print("Sporulation is ON in", round((on_in_attractor / (on_in_attractor + off_in_attractor)) * 100.0, 2), "% of attractor states.")

import graphviz graphviz.Source(attractors[0].to_bdd().to_dot(stg.bdd_variables()))

for v in graph.variables(): if len(graph.regulators(v)) == 0: model.set_update_function(v, None)

stg = SymbolicAsyncGraph(model) stg.unit_colored_vertices()

attractors = find_attractors(stg) attractors

shared_colors = attractors[0].colors().intersect(attractors[1].colors()) print("Number of colors in both attractors:", shared_colors.cardinality())

attractor = attractors[0].union(attractors[1]) classes = classify_attractor(stg, attractor) classes

stable_attractor = attractor.intersect_colors(classes["stability"]) disordered_attractor = attractor.intersect_colors(classes["disorder"]) print(stable_attractor) print(disordered_attractor)

sporulation_on = stg.fix_variable("sporulation", True) on_in_stable_attractor = stable_attractor.intersect(sporulation_on).vertices().cardinality() off_in_stable_attractor = stable_attractor.minus(sporulation_on).vertices().cardinality() print("Sporulation is ON in", on_in_stable_attractor, "stable states.") print("Sporulation is OFF in", off_in_stable_attractor, "stable states.") print("Sporulation is ON in", round((on_in_stable_attractor / (on_in_stable_attractor + off_in_stable_attractor)) * 100.0, 2), "% of stable attractor states.") on_in_disorder_attractor = disordered_attractor.intersect(sporulation_on).vertices().cardinality() off_in_disorder_attractor = disordered_attractor.minus(sporulation_on).vertices().cardinality() print("Sporulation is ON in", on_in_disorder_attractor, "disorder states.") print("Sporulation is OFF in", off_in_disorder_attractor, "disorder states.") print("Sporulation is ON in", round((on_in_disorder_attractor / (on_in_disorder_attractor + off_in_disorder_attractor)) * 100.0, 2), "% of disordered attractor states.")

witness = stg.pick_witness(classes["stability"]) witness.to_aeon()

Path("stable_attractor.bdd").write_text(stable_attractor.to_bdd().to_raw_string()) Path("disordered_attractor.bdd").write_text(disordered_attractor.to_bdd().to_raw_string())

stable_reloaded = stg.empty_colored_vertices().copy_with_raw_string(Path("stable_attractor.bdd").read_text()) disordered_reloaded = stg.empty_colored_vertices().copy_with_raw_string(Path("disordered_attractor.bdd").read_text()) print(stable_reloaded) print(disordered_reloaded)

vertex = stg.unit_colored_vertices().pick_vertex() print("Vertex", vertex.vertices().vertices()) basin = reach_bwd(stg, vertex) print("Basin", basin) scc = reach_fwd(stg, vertex, basin) print("SCC", scc)