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)
    • PysbPreassembler
  • Base Agents (indra.assemblers.pysb.base_agents)
    • BaseAgent
    • BaseAgentSet
  • A utility to get graphs from kappa (indra.assemblers.pysb.kappa_util)
    • cm_json_to_graph()
    • cm_json_to_networkx()
    • get_cm_cycles()
    • im_json_to_graph()
• Cytoscape networks (indra.assemblers.cx.assembler)
  • CxAssembler
    • CxAssembler.statements
    • CxAssembler.network_name
    • CxAssembler.cx
    • CxAssembler.add_statements()
    • CxAssembler.make_model()
    • CxAssembler.print_cx()
    • CxAssembler.save_model()
    • CxAssembler.set_context()
    • CxAssembler.upload_model()
  • NiceCxAssembler
    • NiceCxAssembler.network
    • NiceCxAssembler.add_edge()
    • NiceCxAssembler.add_node()
    • NiceCxAssembler.make_model()
    • NiceCxAssembler.print_model()
• Natural language (indra.assemblers.english.assembler)
  • AgentWithCoordinates
    • AgentWithCoordinates.update_coords()
  • EnglishAssembler
    • EnglishAssembler.statements
    • EnglishAssembler.model
    • EnglishAssembler.stmt_agents
    • EnglishAssembler.add_statements()
    • EnglishAssembler.make_model()
  • SentenceBuilder
    • SentenceBuilder.agents
    • SentenceBuilder.sentence
    • SentenceBuilder.append()
    • SentenceBuilder.append_as_list()
    • SentenceBuilder.append_as_sentence()
    • SentenceBuilder.make_sentence()
    • SentenceBuilder.prepend()
  • english_join()
  • statement_base_verb()
  • statement_passive_verb()
  • statement_present_verb()
• 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)
  • SifAssembler
    • SifAssembler.graph
    • SifAssembler.make_model()
    • SifAssembler.print_boolean_net()
    • SifAssembler.print_loopy()
    • SifAssembler.print_model()
    • SifAssembler.save_model()
• MITRE “index cards” (indra.assemblers.index_card.assembler)
  • IndexCardAssembler
    • IndexCardAssembler.statements
    • IndexCardAssembler.add_statements()
    • IndexCardAssembler.make_model()
    • IndexCardAssembler.print_model()
    • IndexCardAssembler.save_model()
• SBGN output (indra.assemblers.sbgn.assembler)
  • SBGNAssembler
    • SBGNAssembler.statements
    • SBGNAssembler.sbgn
    • SBGNAssembler.add_statements()
    • SBGNAssembler.make_model()
    • SBGNAssembler.print_model()
    • SBGNAssembler.save_model()
• Cytoscape JS networks (indra.assemblers.cyjs.assembler)
  • CyJSAssembler
    • CyJSAssembler.statements
    • CyJSAssembler.add_statements()
    • CyJSAssembler.get_gene_names()
    • CyJSAssembler.make_model()
    • CyJSAssembler.print_cyjs_context()
    • CyJSAssembler.print_cyjs_graph()
    • CyJSAssembler.save_json()
    • CyJSAssembler.save_model()
    • CyJSAssembler.set_CCLE_context()
• Tabular output (indra.assemblers.tsv.assembler)
  • TsvAssembler
    • TsvAssembler.statements
    • TsvAssembler.make_model()
• HTML browsing and curation (indra.assemblers.html.assembler)
  • DB_TEXT_COLOR
  • READER_TEXT_COLOR
  • generate_source_css()
  • HtmlAssembler
    • HtmlAssembler.statements
    • HtmlAssembler.model
    • HtmlAssembler.metadata
    • HtmlAssembler.ev_counts
    • HtmlAssembler.beliefs
    • HtmlAssembler.db_rest_url
    • HtmlAssembler.add_statements()
    • HtmlAssembler.make_json_model()
    • HtmlAssembler.make_model()
    • HtmlAssembler.append_warning()
    • HtmlAssembler.save_model()
  • src_url()
  • tag_text()
• 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)
  • PybelAssembler
    • PybelAssembler.save_model()
    • PybelAssembler.to_database()
    • PybelAssembler.to_web()
  • get_causal_edge()
• Kami models (indra.assemblers.kami.assembler)
  • KamiAssembler
    • KamiAssembler.make_model()
  • Nugget
    • Nugget.add_agent()
    • Nugget.add_edge()
    • Nugget.add_node()
    • Nugget.add_typing()
    • Nugget.get_nugget_dict()
    • Nugget.get_typing_dict()
• IndraNet Graphs (indra.assemblers.indranet)
  • IndraNet
    • IndraNet.digraph_from_df()
    • IndraNet.from_df()
    • IndraNet.signed_from_df()
    • IndraNet.to_digraph()
    • IndraNet.to_signed_graph()
  • IndraNetAssembler
    • IndraNetAssembler.model
    • IndraNetAssembler.add_statements()
    • IndraNetAssembler.make_df()
    • IndraNetAssembler.make_model()
    • IndraNetAssembler.make_model_by_preassembly()
    • IndraNetAssembler.make_model_from_df()
  • get_ag_ns_id()