BEvis_conf.yaml

# BEvis configuration 
#
## step_1: import packages and upload models.
#==============================================
# User input:
#
step1:
    models_directory: './models_sbml3' # Change to sbml models directory.

# step_2: prepare data for COMETS
#==============================================
# User input:
#
step2:
    input_dir: './data/' # Change to input directory location.
    nc: 20 #set number of days from day max
    met_size_log_factor: 10000000
    met_size_over_all_factor: 20
#==============================================

# step_3: preparing a dictionary of bacterium and compound (with carbon only) as key,and flux as value, for a selected day.
#==============================================
# uptake_of_interest:
# Make a list of important compounds to uptake. Use model compound name format.
# User input:
step3:
#day: 90 # selected day (cycle) to explore.
    output_dir: './results/' # location of output files.
    uptake_of_interest: ['Ethylenzene', 'Benzene', 'o-Xylene', 'Toluol']
    secretions_of_interest: ['CO2','Methane']
    #uptake_of_interest: ['Ethylenzene_C8H10', 'Benzene_C6H6', 'o-Xylene_C8H10', 'Toluol_C7H8']
    #secretions_of_interest: ['CO2_CO2','Methane_CH4']

# step_4: Preparing  a dictionary for bacteria biomass, and compound amount, in the selected day, for using as nodes size.
#==============================================
# User input:
step4:
    bm_factor: 1E+12 # change according node size requested.
    met_factor: 1E+6 # change according node size requested.

# step_5: define edges width, define vertical groups (layers) of bacteria and metabolites, and define color and size of nodes.
#==============================================
# User input:
step5:
# change according edges width requested. Bigger number will cause thinner arrow.
        edges_factor_to_devide: 3

# vertical groups (layers)


# BTEX_degradors # layer 1

        bac_A: ['Thermincola_ferriacetica',
'Geobacter_metallireducens_GS-15',
'Tepidimonas_charontis',
'Desulfomicrobium_baculatum',
'Dechloromonas_aromatica',
'Hydrogenophaga_aromaticivorans',
'Clostridium_fungisolvens',
'Magnetospirillum_magneticum']

# Fermentors layer 3

        bac_B: ['Gudongella_oleilytica',
'Parabacteroides_goldsteinii',
'Longilinea_sp.',
'Geovibrio_thiophilus',
'Mariniplasma_anaerobium',
'Dielma_fastidiosa_AF31',
'Mesotoga_infera']

# Methanogens # layer 5
        bac_C: ['Methanobacterium_formicicum', 'Methanosarcina_acetivorans']

#==============================================

# step_6: create a plot
#==============================================
# User input:
step6:
    plot_filename: 'BEvis.pdf'

#==============================================