Index

A

add_cells() (celltx.biolayer.biolayer.BioLayer method) add_compartment() (celltx.biolayer.biolayer.BioLayer method) (celltx.syslayer.syslayer.SysLayer method) add_compartment_linkage() (celltx.syslayer.syslayer.SysLayer method) add_cytokine() (celltx.biolayer.biolayer.BioLayer method) add_edge() (celltx.graphlayer.graphlayer.GraphLayer method) add_element() (celltx.syslayer.syslayer.SysLayer method)

add_interaction() (celltx.biolayer.biolayer.BioLayer method) add_node() (celltx.graphlayer.graphlayer.GraphLayer method) add_relationship() (celltx.syslayer.syslayer.SysLayer method) add_tx_cell_killtarget() (celltx.biolayer.biolayer.BioLayer method) add_tx_cells() (celltx.biolayer.biolayer.BioLayer method) add_tx_cytokine_interaction() (celltx.biolayer.biolayer.BioLayer method) add_tx_state_linkage() (celltx.biolayer.biolayer.BioLayer method)

B

bio (celltx.model.Model attribute), [1]

BioLayer (class in celltx.biolayer.biolayer)

C

cells (celltx.biolayer.biolayer.BioLayer attribute) celltx module, [1] celltx.biolayer module celltx.biolayer.biolayer module celltx.functions module, [1] celltx.graphlayer module celltx.graphlayer.graphlayer module celltx.model module, [1] celltx.modeller module, [1] celltx.odelayer module celltx.odelayer.odelayer module

celltx.syslayer module celltx.syslayer.syslayer module celltx.util module, [1] chunks() (celltx.odelayer.odelayer.ODELayer method) compartment_graph() (celltx.model.Model method), [1] compartment_linkages (celltx.biolayer.biolayer.BioLayer attribute) compartments (celltx.biolayer.biolayer.BioLayer attribute) compose() (celltx.biolayer.biolayer.BioLayer method) (celltx.syslayer.syslayer.SysLayer method) compose_ode_system() (celltx.graphlayer.graphlayer.GraphLayer method) configure_model() (celltx.modeller.Modeller method), [1] Constant (class in celltx.functions), [1] constant() (celltx.biolayer.biolayer.BioLayer method) convert_bio_func_to_sys() (celltx.biolayer.biolayer.BioLayer method) convert_bio_sel_to_sys() (celltx.biolayer.biolayer.BioLayer method) convert_sys_func_to_graph() (celltx.syslayer.syslayer.SysLayer method) convert_sys_sel_to_graph() (celltx.syslayer.syslayer.SysLayer method) cytokines (celltx.biolayer.biolayer.BioLayer attribute)

D

default_assumptions (celltx.functions.Constant attribute), [1] (celltx.functions.Selector attribute), [1] (celltx.functions.Symbol attribute), [1]

display_args() (celltx.odelayer.odelayer.ODELayer method) display_equations() (celltx.odelayer.odelayer.ODELayer method)

E

execute_argspace_search() (celltx.odelayer.odelayer.ODELayer method)

execute_paramspace_search() (celltx.odelayer.odelayer.ODELayer method)

F

format_timedelta() (in module celltx.util), [1]

G

gen_argspace_samples() (celltx.odelayer.odelayer.ODELayer method) gen_ode_model() (celltx.odelayer.odelayer.ODELayer method) gen_paramspace_samples() (celltx.odelayer.odelayer.ODELayer method) gen_states_for_tx_cell() (celltx.biolayer.biolayer.BioLayer method) (celltx.syslayer.syslayer.SysLayer method) generate_graph() (celltx.graphlayer.graphlayer.GraphLayer method) get_adjacent_compartments() (celltx.biolayer.biolayer.BioLayer method) get_cells() (celltx.biolayer.biolayer.BioLayer method) get_cytokine() (celltx.biolayer.biolayer.BioLayer method) get_edge() (celltx.graphlayer.graphlayer.GraphLayer method)

get_element() (celltx.syslayer.syslayer.SysLayer method) get_element_state() (celltx.syslayer.syslayer.SysLayer method) get_model() (celltx.modeller.Modeller static method), [1] get_model_options() (celltx.modeller.Modeller method), [1] get_node() (celltx.graphlayer.graphlayer.GraphLayer method) get_param_value() (celltx.odelayer.odelayer.ODELayer method) get_species() (celltx.biolayer.biolayer.BioLayer method) get_tx_cellstate() (celltx.biolayer.biolayer.BioLayer method) get_tx_celltype() (celltx.biolayer.biolayer.BioLayer method) graph (celltx.model.Model attribute), [1] GraphLayer (class in celltx.graphlayer.graphlayer)

H

hill() (in module celltx.functions), [1]

I

in_edges_for_node() (celltx.graphlayer.graphlayer.GraphLayer method) index_of_parameter() (celltx.odelayer.odelayer.ODELayer method) index_of_species() (celltx.odelayer.odelayer.ODELayer method)

inspect_terms_for_simulation() (celltx.odelayer.odelayer.ODELayer method) integrate() (celltx.odelayer.odelayer.ODELayer method) integrate_quash_species() (celltx.odelayer.odelayer.ODELayer method) interactions (celltx.biolayer.biolayer.BioLayer attribute)

L

link_compartments() (celltx.biolayer.biolayer.BioLayer method)

M

model (celltx.modeller.Modeller attribute), [1] Model (class in celltx.model), [1] model() (celltx.odelayer.odelayer.ODELayer method) model_options (celltx.modeller.Modeller attribute), [1] Modeller (class in celltx.modeller), [1] module celltx, [1] celltx.biolayer celltx.biolayer.biolayer celltx.functions, [1] celltx.graphlayer celltx.graphlayer.graphlayer celltx.model, [1] celltx.modeller, [1] celltx.odelayer celltx.odelayer.odelayer celltx.syslayer celltx.syslayer.syslayer celltx.util, [1]

N

name (celltx.functions.Constant attribute), [1] (celltx.functions.Selector attribute), [1] (celltx.functions.Symbol attribute), [1] (celltx.model.Model attribute), [1]

O

ode (celltx.model.Model attribute), [1]

ODELayer (class in celltx.odelayer.odelayer) out_edges_for_node() (celltx.graphlayer.graphlayer.GraphLayer method)

P

pin_params_for_search() (celltx.odelayer.odelayer.ODELayer method) process_argspace_chunk() (celltx.odelayer.odelayer.ODELayer method)

process_paramset_chunk() (celltx.odelayer.odelayer.ODELayer method) profile_parameter() (celltx.odelayer.odelayer.ODELayer method)

R

ravel_expression() (celltx.odelayer.odelayer.ODELayer method) (in module celltx.functions), [1]

readout_funcs (celltx.modeller.Modeller attribute), [1]

S

Selector (class in celltx.functions), [1] selfloops_for_node() (celltx.graphlayer.graphlayer.GraphLayer method) set_initial_value() (celltx.odelayer.odelayer.ODELayer method) set_initial_value_byname() (celltx.odelayer.odelayer.ODELayer method) set_model_options() (celltx.modeller.Modeller method), [1] set_param_search_range() (celltx.odelayer.odelayer.ODELayer method)

set_param_value() (celltx.odelayer.odelayer.ODELayer method) set_tx_cell_daughter_state() (celltx.biolayer.biolayer.BioLayer method) set_x0_search_range() (celltx.odelayer.odelayer.ODELayer method) setup() (celltx.modeller.Modeller method), [1] Symbol (class in celltx.functions), [1] sys (celltx.model.Model attribute), [1] SysLayer (class in celltx.syslayer.syslayer)

T

tx_cells (celltx.biolayer.biolayer.BioLayer attribute)

V

validate_selector() (celltx.biolayer.biolayer.BioLayer method) (celltx.graphlayer.graphlayer.GraphLayer method) (celltx.syslayer.syslayer.SysLayer method)

visualize_compartments() (celltx.model.Model method), [1]

W

write_graph_dotfile() (celltx.graphlayer.graphlayer.GraphLayer method)