ecoli.analysis.causality_network.read_dynamics
Reads dynamics data for each of the nodes of a causality network from a single simulation.
- ecoli.analysis.causality_network.read_dynamics.array_timeseries(data, path, timeseries)[source]
Converts data of the format {time: {path: value}}} to timeseries of the format {path: [value_1, value_2,…]}. Modifies timeseries in place.
- ecoli.analysis.causality_network.read_dynamics.convert_dynamics(seriesOutDir, sim_data, node_list, edge_list, experiment_id)[source]
Convert the sim’s dynamics data to a Causality seriesOut.zip file.
- ecoli.analysis.causality_network.read_dynamics.read_charging_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for charging nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_complexation_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for complexation nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_equilibrium_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for equilibrium nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_gene_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for gene nodes from simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_global_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads global dynamics from simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_metabolism_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for metabolism nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_metabolite_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dyanmics data for metabolite nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_protein_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for monomer/complex nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_regulation_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for regulation nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_rna_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for transcript (RNA) nodes from simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_rna_maturation_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for RNA maturation nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_tf_binding_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for TF binding nodes from a simulation output.
- ecoli.analysis.causality_network.read_dynamics.read_transcription_dynamics(sim_data, node, node_id, indexes, volume, timeseries)[source]
Reads dynamics data for transcription nodes from simulation output.