Ideas for Rule based modeling

Extending ReactionRule

Annotating ReactionRules

>>> rr = create_unimolecular_reaction_rule(
... Species("g6p"), Species("f6p"), 1.0)
>>> rr.set_attribute("ecnumber", "5.3.1.9")

>>> with reaction_rules():
...     g6p > f6p | 1.0 | {"ecnumber": "5.3.1.9"}

Filtering ReactionRules in a model

>>> m.reaction_rules({"ecnumber": "5.3.1.9"})

Modifying ReactionRules in a model

Definition in ode

Optimization

Parameter sweep

Parameter optimization

Equation determination

Import and export

Format

SBML, BioNetGen, Kappa

Pushing models to a repository

Database connection

Fetching annotations

>>> sp = Species("RpsA")
>>> sp.set_attribute("bnumber", "b0911")
>>> db.description(sp, dbtype="kegg")
'rpsA, 30S ribosomal subunit protein S1.'

Accessing references (evidences)

Fetching entries and generating components

Fetching models

Analysis and visualization

Evaluating flux

>>> w.evaluate(rr)

Visualizing components

>>> sp = Species("EGFR(Y1068=P^1).Grb2(SH2^1)")
>>> rr = create_unbinding_reaction_rule(
... Species("EGFR(Y1068=P^1).Grb2(SH2^1)"),
... Species("EGFR(Y1068=P)"), Species("Grb2(SH2)"), 1.0)
>>> viz.diagram(sp)
>>> viz.diagram(rr)

Visualizing a model