Assemblers of model output (indra.assemblers
)¶
- Executable PySB models (
indra.assemblers.pysb.assembler
)- PySB Assembler (
indra.assemblers.pysb.assembler
)Param
Policy
PysbAssembler
UnknownPolicyError
add_rule_to_model()
complex_monomers_default()
complex_monomers_one_step()
get_agent_rule_str()
get_annotation()
get_create_parameter()
get_grounded_agents()
get_monomer_pattern()
get_site_pattern()
get_uncond_agent()
grounded_monomer_patterns()
parse_identifiers_url()
set_base_initial_condition()
set_extended_initial_condition()
- PySB PreAssembler (
indra.assemblers.pysb.preassembler
) - Base Agents (
indra.assemblers.pysb.base_agents
) - A utility to get graphs from kappa (
indra.assemblers.pysb.kappa_util
)
- PySB Assembler (
- Cytoscape networks (
indra.assemblers.cx.assembler
) - Natural language (
indra.assemblers.english.assembler
) - Node-edge graphs (
indra.assemblers.graph.assembler
)GraphAssembler
GraphAssembler.statements
GraphAssembler.graph
GraphAssembler.existing_nodes
GraphAssembler.existing_edges
GraphAssembler.graph_properties
GraphAssembler.node_properties
GraphAssembler.edge_properties
GraphAssembler.add_statements()
GraphAssembler.get_string()
GraphAssembler.make_model()
GraphAssembler.save_dot()
GraphAssembler.save_pdf()
- SIF / Boolean networks (
indra.assemblers.sif.assembler
) - MITRE “index cards” (
indra.assemblers.index_card.assembler
) - SBGN output (
indra.assemblers.sbgn.assembler
) - Cytoscape JS networks (
indra.assemblers.cyjs.assembler
) - Tabular output (
indra.assemblers.tsv.assembler
) - HTML browsing and curation (
indra.assemblers.html.assembler
) - BMI wrapper for PySB-assembled models (
indra.assemblers.pysb.bmi_wrapper
)BMIModel
BMIModel.export_into_python()
BMIModel.finalize()
BMIModel.get_attribute()
BMIModel.get_current_time()
BMIModel.get_input_var_names()
BMIModel.get_output_var_names()
BMIModel.get_start_time()
BMIModel.get_status()
BMIModel.get_time_step()
BMIModel.get_time_units()
BMIModel.get_value()
BMIModel.get_values()
BMIModel.get_var_name()
BMIModel.get_var_rank()
BMIModel.get_var_type()
BMIModel.get_var_units()
BMIModel.initialize()
BMIModel.make_repository_component()
BMIModel.set_value()
BMIModel.set_values()
BMIModel.update()
- PyBEL graphs (
indra.assemblers.pybel.assembler
) - Kami models (
indra.assemblers.kami.assembler
) - IndraNet Graphs (
indra.assemblers.indranet
)