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config
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config
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# Gitsbe config file (tab-delimited)
# Parameter: Value
### Global
# Output verbosity level (0 = nothing - 3 = everything)
verbosity: 3
# Delete all files in *_tmp dirs
delete_tmp_files: true
# If true, it will compress the log and tmp files
compress_log_and_tmp_files: true
# Run simulations in parallel
use_parallel_sim: true
# The number (>1) of simulations to execute in parallel
# The standard value would be to have as many parallel simulations as the
# machine's Cores (reduce it if too many parallel simulations are causing issues)
parallel_sim_num: 4
# Tool to use for the calculation of attractors
# Supported values: bnet_reduction, bnet_reduction_reduced, biolqm_stable_states, biolqm_trapspaces, mpbn_trapspaces
attractor_tool: biolqm_stable_states
### Gitsbe section
## Model trimming
remove_output_nodes: false
remove_input_nodes: true
## Exporting input network file
export_to_gitsbe: true
export_to_sif: true
export_to_ginml: true
export_to_sbml_qual: false
export_to_boolnet: false
# Parameters for evolutionary algorithms
# Number of simulations (evolutions) to run
simulations: 50
# Number of generations per simulation (or less if target_fitness is reached, see below)
generations: 20
# Number of models per generation
population: 20
# Number of crossovers
crossovers: 1
# Number of models selected for next generation
selection: 3
# Type of mutations to introduce and a value that corresponds to the number of
# (randomly selected) boolean equations that the specific mutation is going
# to be applied to
balance_mutations: 3
random_mutations: 0
shuffle_mutations: 0
topology_mutations: 0
# Target fitness threshold to stop evolution (1 is the absolute maximum value)
target_fitness: 0.99
# Factor to multiply number of mutations until initial phase is over (>0 stable states obtained)
bootstrap_mutations_factor: 1000
# Factor to multiply number of mutations after initial phase is over (>0 stable states obtained)
mutations_factor: 1
# Factor to multiply number of regulator priority shuffles until initial phase is over
bootstrap_shuffle_factor: 0
# Factor to multiply number of regulator priority shuffles after initial phase is over
shuffle_factor: 0
# Factor to multiply number of topology mutations until initial phase is over
bootstrap_topology_mutations_factor: 5
# Factor to multiply number of topology mutations after initial phase is over
topology_mutations_factor: 1
# Number of models to save
models_saved: 3
# Additional formats to export best models (gitsbe format is enabled by default)
best_models_export_to_ginml: false
best_models_export_to_sbml_qual: false
best_models_export_to_boolnet: false
# Threshold for saving models
fitness_threshold: 0.1
### Drabme section
# Creates all combinations of drugs from the drugpanel file up to and including
# this size (only used when there is no perturbations file)
max_drug_comb_size: 2
# method to use for the calculation of synergies ensemblewise and modelwise
synergy_method: hsa