vivarium.compartments.gene_expression module

class vivarium.compartments.gene_expression.GeneExpression(config)

Bases: vivarium.core.process.Generator

defaults = {'complexation': {}, 'degradation': {}, 'global_path': ('global',), 'initial_mass': <Quantity(1339.0, 'femtogram')>, 'time_step': 1.0, 'transcription': {}, 'translation': {}}

generate_processes(config)

generate_topology(config)

vivarium.compartments.gene_expression.gene_network_plot(data, out_dir, filename='gene_network')

Make a gene network plot from configuration data

• data (dict):

  { ‘operons’: operons, the “genes” in a chromosome config with {operon: [genes list]} ‘templates’: promoters, the “promoters” in a chromosome config with {promoter: {sites: [], thresholds: []}} ‘complexes’: complexes, stoichiometry from a complexation process. }

vivarium.compartments.gene_expression.plot_gene_expression_output(timeseries, config, out_dir='out')

vivarium.compartments.gene_expression.run_gene_expression(total_time=10, out_dir='out')

vivarium.compartments.gene_expression.test_gene_expression(total_time=10)