################################################### # BioJazz configuration ################################################### #---------------------------------------- # CPU AND CLUSTER SETTINGS #---------------------------------------- cluster_type = LOCAL cluster_size = 1 nice = 15 vmem = 200000000 #---------------------------------------- # WORKSPACE AND CUSTOM SCORING MODULES #---------------------------------------- scoring_class = Ultrasensitive work_dir = ultrasensitive local_dir = ultrasensitive/localdir initial_genome = random #initial_genome = load test/custom/Ultrasensitive.obj #---------------------------------------- # GENOME PARAMS #---------------------------------------- # Scaling: all concentrations in uM, all 2nd-order rates in uM^-1 s^-1 # Genome class radius = 3 # should be reasonable. Binomial[Width,radius..0]/2^width kf_max = 1e3 # uM^-1 s^-1 kf_min = 1e-3 kb_max = 1e3 kb_min = 1e-3 kp_max = 1e3 kp_min = 1e-3 # Gene class regulated_concentration_width = 10 gene_unused_width = 4 regulated_concentration_max = 1e3 # 1mM regulated_concentration_min = 1e-3 # 1nM ~ 1 molecule in prokaryote # Domain class RT_transition_rate_width = 10 TR_transition_rate_width = 10 RT_phi_width = 10 domain_unused_width = 4 RT_transition_rate_max = 1e2 RT_transition_rate_min = 1e-2 TR_transition_rate_max = 1e2 TR_transition_rate_min = 1e-2 RT_phi_max = 1.0 RT_phi_min = 0.0 # ProtoDomain class binding_profile_width = 10 kf_profile_width = 20 kb_profile_width = 20 kp_profile_width = 10 steric_factor_profile_width = 20 Keq_profile_width = 10 protodomain_unused_width = 4 Keq_ratio_max = 1e2 Keq_ratio_min = 1e-2 #---------------------------------------- # EVOLUTION PARAMS #---------------------------------------- num_generations = 10000 target_score = 0.8 first_generation = 0 # define the number of the first generation, either 0 or 1 continue_sim = 0 continue_init = 0 remove_old_files = 1 score_initial_generation = 1 rescore_elite = 0 report_on_fly = 1 report_selection = 0 # because of fossil_epoch you may lose information if collect information later!! # selection method: kimura selection selection_method = kimura_selection effective_population_size = 1e8 # for kimura_selection only amplifier_alpha = 1e3 # for kimura_selection only, speed up the evolution, range: The lowe bound is 1.16 the upper bound is 2*effective_population_size max_mutate_attempts = 100000 # default -1 or not defined as unlimited, should be an integer; # selection method: population-based selection #selection_method = population_based_selection #fossil_epoch = 10 # for genome storage and records of genomes in certain generations, comment if using kimura selectio method (must) or record every generation #inum_genomes = 50 # for kimura selection method, doesn't matter because it's set 1 as default. #evolve_population = 1000 # for population-based selection method only #mutation_rate = 0.05 # For population-based model # mutation settings mutation_rate_params = 0.0 mutation_rate_global = 0.01 gene_duplication_rate = 0.005 gene_deletion_rate = 0.005 domain_duplication_rate = 0.005 domain_deletion_rate = 0.005 recombination_rate = 0.01 hgt_rate = 0.01 # currently not implemented yet #---------------------------------------- # ANALYSIS PARAMS (POST-EVOLUTION) #---------------------------------------- #report_on_collection = 1 # for population based method usually set as 1 !!(Currently not implemented) restore_genome = 0 analysis_dir = analysis ################################################### # User-defined, application-specific configuration ################################################### #---------------------------------------- # ANC PARAMS #---------------------------------------- max_external_iterations = -1 max_internal_iterations = -1 max_complex_size = 3 #MATLAB has maximal length of names, if using MATLAB as simulator, this value should always be less than 9. Either -1(unlimited) or 6 should be resonable, please ref the Plos ONE paper from Vincent Danos group. max_species = 512 max_csite_bound_to_msite_number = 1 # originally set as 1, but if consider more complex situation, we should put this unlimited, which means in complex multiple csite-msite bindings could happen. default_max_count = 2 # this prevents polymerization (see ANC manual) default_steric_factor = 1000 # in micro-mol/L export_graphviz = nothing #export_graphviz = network,collapse_states,collapse_complexes #export_graphviz = network,collapse_states,collapse_complexes,primary,scalar,ungrouped,canonical # possibly there are more information could be output #---------------------------------------- # FACILE/MATLAB SETTINGS #---------------------------------------- solver = ode23s #solver = stoch sampling_interval = 1.0 SS_timescale = 500.0 # MATLAB odeset params InitialStep = 1e-8 AbsTol = 1e-9 RelTol = 1e-3 MaxStep = 500.0 #---------------------------------------- # SIMULATION/SCORING PARAMS #---------------------------------------- plot_input = 1 plot_output = 1 plot_species = 0 plot_phase = 1 plot_min = -1 round_values_flag = 0 steady_state_threshold = 1000 # IC settling time steady_state_score_threshold = 0.5 delta_threshold = 0.01 # relative measure of amplitude used to filter out integration noise amplitude_threshold = 0.01 # absolute measure of amplitude ultrasensitivity_threshold = 5 # ratio of 2nd step over 1st step complexity_threshold = 250 expression_threshold = 500 w_n = 0.0 w_c = 0.0 # complexity score weight w_e = 0.0 w_s = 1.0 w_a = 1.0 w_u = 1.0 w_u1 = 1.0 w_u3 = 1.0 LG_range = 10 # uM (about 6 molecules in 1e-18L vol ???) LG_delay = ~ LG_strength = 4.0 # in Hz LG_ramp_time = 3000 LG_steps = 3 LG_timeout = 20000 #stimulus = staircase_equation #stimulus = ramp_equation stimulus = ss_ramp_equation #hill_n = 8 hill_n = 40 hill_k = 5 TG_init = 1000 # uM cell_volume = 1e-18 # 1e-18L --> sub-cellular volume # to make sure the input and output have relatively large distance and also have relative large distance from themselves # and also make sure their binding partner to have relatively large distance in this case the intermediate binding profile could be 0010110100 have both 5 distanct to all four binding profiles # it depends the problem, whether want far distances between initial profiles or shorter distances lg_binding_profile = 0100111010 tg_binding_profile = 0111000110 #---------------------------------------- # SPREADSHEET EXPORT/ANALYSIS #---------------------------------------- genome_attribute_names = \ score, \ ultrasensitivity_score, \ expression_score, \ amplitude_score, \ complexity_score, \ steady_state_score, \ complexity,\ num_anc_species,\ num_rules,\ num_genes,\ num_pruned_genes,\ num_domains,\ num_protodomains,\ num_allosteric_domains,\ num_allosteric_protodomains,\ num_binding_protodomains,\ num_phosphorylation_protodomains,\ num_catalytic_protodomains,\ num_kinase_protodomains,\ num_phosphatase_protodomains,\ num_adjacent_kinases,\ num_adjacent_phosphatases,\ num_receptive_protodomains,\ tg_K1,\ tg_K2,\ tg_K1_concentration,\ tg_K2_concentration,\