SIF / Boolean networks (
- class indra.assemblers.sif.assembler.SifAssembler(stmts=None)
The SIF assembler assembles INDRA Statements into a networkx graph.
This graph can then be exported into SIF (simple interaction format) or a Boolean network.
stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be added to the assembler’s list of Statements.
A networkx graph that is assembled by this assembler.
- make_model(use_name_as_key=False, include_mods=False, include_complexes=False)
Assemble the graph from the assembler’s list of INDRA Statements.
use_name_as_key (boolean) – If True, uses the name of the agent as the key to the nodes in the network. If False (default) uses the matches_key() of the agent.
include_mods (boolean) – If True, adds Modification statements into the graph as directed edges. Default is False.
include_complexes (boolean) – If True, creates two edges (in both directions) between all pairs of nodes in Complex statements. Default is False.
Return a Boolean network from the assembled graph.
See https://github.com/ialbert/booleannet for details about the format used to encode the Boolean rules.
Return a SIF string of the assembled model.
include_unsigned_edges (bool) – If True, includes edges with an unknown activating/inactivating relationship (e.g., most PTMs). Default is False.
- save_model(fname, include_unsigned_edges=False)
Save the assembled model’s SIF string into a file.