KarrLab/rand_wc_model_gen

[rand_wc_model_gen]
    
    [[kb_gen]]
        id = rand_wc_model
        name = Random whole-cell model
        version = ${version}
        data_repo_metadata = true

        [[[component]]]
            [[[[PropertiesGenerator]]]]
                mean_volume = 1e-15
                mean_fraction_dry_weight = 0.3
                mean_doubling_time = 1800.
                mean_cell_density = 1e6
            
            [[[[GenomeGenerator]]]]
                num_chromosomes = 1
                chromosome_topology = circular
                mean_gc_frac = 0.5
                mean_num_genes = 4377. # Escherichia coli K-12
                mean_gene_len = 924. # DOI: 10.1093/molbev/msk019
                mean_coding_frac = 0.88 # DOI: 10.1007/s10142-015-0433-4
                translation_table = 1
                seq_path = ${package_path}/kb/seq.fna

            [[[MetabolitesGenerator]]]
                data_path = ${package_path}/data/metabolites.csv

            [[[ObservablesGenerator]]]
                translation_table = 1
            

    [[kb]]
        [[[path]]]
            core = ${package_path}/kb/core.xlsx
            seq = ${package_path}/kb/seq.fna

    [[model_gen]]
        id = rand_wc_model
        name = Random whole-cell model
        version = ${version}
        data_repo_metadata = true

        [[[component]]]
            [[[[TranscriptionSubmodelGenerator]]]]
            
            [[[[RnaDegradationSubmodelGenerator]]]]

    [[model]]
        path = ${package_path}/model/model.xlsx

    [[sim]]
        end_time = 3600
        time_step = 1
        seed = 0

    [[sim_results]]
        checkpoint_period = 1
        path = ${package_path}/sim_results/

    [[analysis]]
        path = ${package_path}/analysis/