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A
abs
(in
SloppyCell.lmopt
)
add_species()
(in
Network
)
append()
(in
KeyedList
)
add_algebraic_rule()
(in
Network
)
AddAmplitudeCheck()
(in
Experiment
)
append()
(in
Trajectory
)
add_assignment_rule()
(in
Network
)
AddCalculation()
(in
CalculationCollection
)
appendFromODEINT()
(in
Trajectory
)
add_compartment()
(in
Network
)
addCompartment()
(in
Network
)
appendSensFromODEINT()
(in
Trajectory
)
add_constraint()
(in
Network
)
addConstraint()
(in
Network
)
approx_fhess_p()
(in
SloppyCell.lmopt
)
add_event()
(in
Network
)
addEvent()
(in
Network
)
approx_fprime()
(in
SloppyCell.lmopt
)
add_event_info()
(in
Trajectory
)
AddExperiment()
(in
ExperimentCollection
)
approx_fprime1()
(in
SloppyCell.lmopt
)
add_func_def()
(in
Network
)
addParameter()
(in
Network
)
approx_fprime2()
(in
SloppyCell.lmopt
)
add_integral_data()
(in
Experiment
)
AddPeriodCheck()
(in
Experiment
)
args_to_remove
(in
SloppyCell
)
add_parameter()
(in
Network
)
addReaction()
(in
Network
)
AST
(in
SloppyCell.ExprManip
)
add_rate_rule()
(in
Network
)
AddResidual()
(in
Model
)
attach_observer()
(in
Model
)
add_scaled_max()
(in
Experiment
)
addSpecies()
(in
Network
)
autocorrelation()
(in
SloppyCell.Ensembles
)
add_scaled_min()
(in
Experiment
)
AmplitudeCheckResidual
(in
SloppyCell.Residuals
)
B
basic_colors
(in
SloppyCell.Plotting
)
BestMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
build_interpolated_traj()
(in
Trajectory
)
basic_lines
(in
SloppyCell.Plotting
)
bootstrap()
(in
SloppyCell.Utility
)
Bunch
basic_symbols
(in
SloppyCell.Plotting
)
build_failure
(in
SloppyCell.make_htdocs
)
C
C()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
CalculateForAllDataPoints()
(in
Model
)
ComputeInternalVariableDerivs()
(in
Model
)
calcCovarianceMat()
(in
SloppyCell.Vandermonde.VdmPairwise
)
CalculateSensitivitiesForAllDataPoints()
(in
Model
)
ComputeInternalVariables()
(in
Model
)
calcDmat()
(in
SloppyCell.Vandermonde.VdmPairwise
)
CalculateSensitivity()
(in
CalculationCollection
)
config
(in
SloppyCell.setup
)
CalcHessian()
(in
Model
)
CalculateSensitivity()
(in
Network
)
ConstraintEvent
(in
SloppyCell.ReactionNetworks.Components
)
CalcHessianInLogParameters()
(in
Model
)
CalculationCollection
(in
SloppyCell.Collections
)
ConstraintViolatedException
(in
SloppyCell.Utility
)
calcLambdaMat_1()
(in
SloppyCell.Vandermonde.VdmPairwise
)
change_stoichiometry()
(in
Reaction
)
ConstructionReaction
calcLambdaMat_2()
(in
SloppyCell.Vandermonde.VdmPairwise
)
check_grad()
(in
SloppyCell.lmopt
)
CoPromoterReaction
calcLambdaMat_3()
(in
SloppyCell.Vandermonde.VdmPairwise
)
checkLambda()
(in
SloppyCell.Vandermonde.VdmPairwise
)
copy()
(in
KeyedList
)
calcLambdaMat_4()
(in
SloppyCell.Vandermonde.VdmPairwise
)
chisq()
(in
Model
)
copy()
(in
Model
)
CalcParameterResponseToResidualArray()
(in
Model
)
clusterScripts
(in
SloppyCell.Vandermonde
)
copy()
(in
Network
)
calcPriors()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
Collections
(in
SloppyCell
)
copy_subset()
(in
Trajectory
)
calcR2mat_1()
(in
SloppyCell.Vandermonde.VdmPairwise
)
colorAlignColumns()
(in
SloppyCell.Vandermonde.VdmPairwise
)
cost()
(in
Model
)
calcR2mat_2()
(in
SloppyCell.Vandermonde.VdmPairwise
)
ColorWheel()
(in
SloppyCell.Plotting
)
cost_log_params()
(in
Model
)
calcR2mat_3()
(in
SloppyCell.Vandermonde.VdmPairwise
)
combine_hessians()
(in
SloppyCell.Utility
)
CostAlongP()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
calcR2mat_4()
(in
SloppyCell.Vandermonde.VdmPairwise
)
Compartment
(in
SloppyCell.ReactionNetworks.Components
)
CostEmailer
(in
SloppyCell.Observers
)
calcR2mat_Terms()
(in
SloppyCell.Vandermonde.VdmPairwise
)
compile()
(in
Model
)
CostPrinter
(in
SloppyCell.Observers
)
CalcResidualResponseArray()
(in
Model
)
compile()
(in
Network
)
createNetworkParameter()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
Calculate()
(in
CalculationCollection
)
Components
(in
SloppyCell.ReactionNetworks
)
currdir
(in
SloppyCell
)
Calculate()
(in
Network
)
compute_scale_factors()
(in
Model
)
calculate()
(in
Network
)
compute_sf_entropy()
(in
Experiment
)
D
daeint()
(in
SloppyCell.daskr
)
Differentiation
(in
SloppyCell.ExprManip
)
Dp()
(in
Residual
)
daeintException
(in
SloppyCell.daskr
)
dintVars()
(in
PriorInLog
)
dp()
(in
Residual
)
daskr
(in
SloppyCell
)
dintVars()
(in
Residual
)
dp()
(in
ScaledErrorInFit
)
daskr
(in
SloppyCell.setup
)
dintVars()
(in
ScaledErrorInFit
)
dp()
(in
ScaledExtremum
)
data_files
(in
SloppyCell.setup
)
disable_c
(in
Network
)
dummy_func()
(in
SloppyCell.daskr
)
decompHess
(in
SloppyCell.Vandermonde
)
disable_c
(in
SloppyCell
)
dy()
(in
PriorInLog
)
deepcopy()
(in
KeyedList
)
disable_debugging_msgs()
(in
SloppyCell.Utility
)
dy()
(in
Residual
)
del_by_key()
(in
KeyedList
)
disable_deriv_funcs()
(in
Network
)
dy()
(in
ScaledErrorInFit
)
design_over_chems()
(in
SloppyCell.ReactionNetworks.OptDesign
)
disable_warnings()
(in
SloppyCell.Utility
)
dyn_var_fixed_point()
(in
Network
)
design_over_single_variance()
(in
SloppyCell.ReactionNetworks.OptDesign
)
doKwargsSubstitution()
(in
Reaction
)
Dynamics
(in
SloppyCell.ReactionNetworks
)
detach_observer()
(in
Model
)
dp()
(in
PriorInLog
)
E
eig()
(in
SloppyCell.Utility
)
evaluate_expr()
(in
Network
)
executeEventAndUpdateSens()
(in
Network
)
enable_debugging_msgs()
(in
SloppyCell.Utility
)
evaluate_interpolated_traj()
(in
Trajectory
)
Experiment
(in
SloppyCell.Collections
)
enable_deriv_funcs()
(in
Network
)
evaluate_interpolated_trajs()
(in
Trajectory
)
ExperimentCollection
(in
SloppyCell.Collections
)
enable_warnings()
(in
SloppyCell.Utility
)
eVec()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
ExponentialDecayReaction
ensemble()
(in
SloppyCell.Ensembles
)
Event
(in
SloppyCell.ReactionNetworks.Components
)
ExprManip
(in
SloppyCell
)
ensemble_log_params()
(in
SloppyCell.Ensembles
)
event_info
(in
SloppyCell.ReactionNetworks.Components
)
extend()
(in
KeyedList
)
ensemble_trajs()
(in
SloppyCell.Ensembles
)
exec_dynamic_functions()
(in
Network
)
extract_vars_cache
(in
SloppyCell.ExprManip.Extraction
)
Ensembles
(in
SloppyCell
)
executeEvent()
(in
Network
)
Extraction
(in
SloppyCell.ExprManip
)
F
failed_args
(in
SloppyCell.ReactionNetworks.Dynamics
)
flush()
(in
Redirector
)
fmin_xform()
(in
SloppyCell.Optimization
)
failed_kwargs
(in
SloppyCell.ReactionNetworks.Dynamics
)
fmin()
(in
SloppyCell.Optimization
)
Force()
(in
Model
)
few_ensemble_trajs()
(in
SloppyCell.Ensembles
)
fmin_lm()
(in
SloppyCell.lmopt
)
free_energy()
(in
Model
)
fill_traj()
(in
Network
)
fmin_lm_log_params()
(in
SloppyCell.Optimization
)
fromSBMLFile()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
findPermutation()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
fmin_lm_scale()
(in
SloppyCell.lmopt
)
fromSBMLString()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
fireEvent()
(in
Network
)
fmin_lmNoJ()
(in
SloppyCell.lmopt
)
full_speed()
(in
Network
)
FirstOrderReaction
fmin_log_params()
(in
SloppyCell.Optimization
)
FunctionDefinition
(in
SloppyCell.ReactionNetworks.Components
)
FixedPointException
fmin_powell_log_params()
(in
SloppyCell.Optimization
)
G
get()
(in
KeyedList
)
get_var_vals()
(in
Network
)
getLambdaR2()
(in
SloppyCell.Vandermonde.VdmPairwise
)
get_c_code()
(in
Network
)
get_var_vals()
(in
Trajectory
)
getMinIndex()
(in
SloppyCell.Vandermonde.VdmPairwise
)
get_calcs()
(in
Model
)
get_var_vals_index()
(in
Trajectory
)
getMinLambdaR2()
(in
SloppyCell.Vandermonde.VdmPairwise
)
get_component_name()
(in
Network
)
get_variable()
(in
Network
)
GetName()
(in
Experiment
)
get_data()
(in
Experiment
)
getAmounts()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetName()
(in
Network
)
get_dynvar_vals()
(in
Trajectory
)
GetAmplitudeChecks()
(in
Experiment
)
GetParameters()
(in
CalculationCollection
)
get_dynvar_vals_index()
(in
Trajectory
)
GetCalculatedValues()
(in
Model
)
GetParameters()
(in
Network
)
get_eqn_structure()
(in
Network
)
GetData()
(in
ExperimentCollection
)
GetParameterTypicalValues()
(in
Network
)
get_expts()
(in
Model
)
getDynamicVarValues()
(in
Network
)
GetPeriodChecks()
(in
Experiment
)
get_fixed_sf()
(in
Experiment
)
getGammas()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetRequiredVarsByCalc()
(in
AmplitudeCheckResidual
)
get_ICs()
(in
Model
)
getHessAA()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetRequiredVarsByCalc()
(in
PeriodCheckResidual
)
get_id()
(in
Network
)
getHessAALogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetRequiredVarsByCalc()
(in
Residual
)
get_initial_velocities()
(in
Network
)
getHessFull()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetRequiredVarsByCalc()
(in
ScaledErrorInFit
)
get_name()
(in
Network
)
getHessFullLogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetRequiredVarsByCalc()
(in
ScaledExtremum
)
get_observers()
(in
Model
)
getHessGG()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetResiduals()
(in
Model
)
get_params()
(in
Model
)
getHessGGLogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetResult()
(in
Network
)
get_sens_array()
(in
SloppyCell.ReactionNetworks.OptDesign
)
GetIntegralDataSets()
(in
Experiment
)
GetScaleFactors()
(in
Model
)
get_sens_vect()
(in
SloppyCell.ReactionNetworks.OptDesign
)
GetInternalVariables()
(in
Model
)
GetSensitivityResult()
(in
Network
)
get_sf_groups()
(in
Experiment
)
GetJacobian()
(in
Model
)
GetValue()
(in
AmplitudeCheckResidual
)
get_shared_sf()
(in
Experiment
)
getJacobian()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
IntegralDataResidual
)
get_times()
(in
Trajectory
)
getJacobianA()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
PeriodCheckResidual
)
get_var_constant()
(in
Network
)
getJacobianALogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
PriorInLog
)
get_var_ic()
(in
Network
)
getJacobianG()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
Residual
)
get_var_ics()
(in
Network
)
getJacobianGLogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
ScaledErrorInFit
)
get_var_traj()
(in
Trajectory
)
getJacobianLog()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetValue()
(in
ScaledExtremum
)
get_var_typical_val()
(in
Network
)
getJacobianLogA()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
GetVarsByCalc()
(in
ExperimentCollection
)
get_var_typical_val()
(in
Trajectory
)
getJacobianLogG()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
global_atol
(in
SloppyCell.ReactionNetworks.Dynamics
)
get_var_typical_vals()
(in
Network
)
getJacobianLogTime()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
global_hmax
(in
SloppyCell.ReactionNetworks.Dynamics
)
get_var_val()
(in
Network
)
GetJandJtJ()
(in
Model
)
global_rtol
(in
SloppyCell.ReactionNetworks.Dynamics
)
get_var_val()
(in
Trajectory
)
GetJandJtJInLogParameters()
(in
Model
)
gradient_log_params_sens()
(in
Model
)
get_var_val_index()
(in
Trajectory
)
GetKey()
(in
Residual
)
gradient_sens()
(in
Model
)
H
has_key()
(in
KeyedList
)
hessian_log_params()
(in
Model
)
HillTransportReaction
HAVE_PYPAR
(in
SloppyCell
)
HeterodimerDissociationReaction
home
(in
SloppyCell.make_htdocs
)
hessian()
(in
Model
)
HeterodimerizationReaction
HomodimerDissociationReaction
hessian_elem()
(in
Model
)
HillDegradationReaction
HomodimerizationReaction
I
imag_cutoff
(in
Model
)
IntegralDataResidual
(in
SloppyCell.Residuals
)
integrateStochastic()
(in
Network
)
import_c_funcs_from_module()
(in
Network
)
integrate()
(in
Network
)
IntegrationException
index_by_key()
(in
KeyedList
)
integrated_var_change()
(in
SloppyCell.ReactionNetworks.OptDesign
)
IO
(in
SloppyCell.ReactionNetworks
)
insert()
(in
KeyedList
)
integrated_var_change_weighted()
(in
SloppyCell.ReactionNetworks.OptDesign
)
items()
(in
KeyedList
)
insert_item()
(in
KeyedList
)
integrateSensitivity()
(in
Network
)
J
Jacobian()
(in
Model
)
jacobian_log_params_sens()
(in
Model
)
jacobian_fd()
(in
Model
)
jacobian_sens()
(in
Model
)
K
KeyedList
(in
SloppyCell.KeyedList_mod
)
keys()
(in
KeyedList
)
KeyedList_mod
(in
SloppyCell
)
keys()
(in
Trajectory
)
L
last_dynamic_var_values()
(in
Trajectory
)
logger
(in
SloppyCell.ExprManip.Differentiation
)
logger
(in
SloppyCell.ReactionNetworks.Plotting
)
leastsq_log_params()
(in
SloppyCell.Optimization
)
logger
(in
SloppyCell.Model_mod
)
logger
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
lmopt
(in
SloppyCell
)
logger
(in
SloppyCell.Optimization
)
logger
(in
SloppyCell.ReactionNetworks.Trajectory_mod
)
load()
(in
SloppyCell.Utility
)
logger
(in
SloppyCell.ReactionNetworks.Components
)
logger
(in
SloppyCell.RunInParallel
)
logger
(in
SloppyCell.Collections
)
logger
(in
SloppyCell.ReactionNetworks.Dynamics
)
logger
(in
SloppyCell.daskr
)
logger
(in
SloppyCell.Ensembles
)
logger
(in
SloppyCell.ReactionNetworks.PerfectData
)
logger
(in
SloppyCell
)
M
make_func_defs()
(in
Network
)
MAX_STEPS
(in
SloppyCell.ReactionNetworks.Dynamics
)
Model
(in
SloppyCell.Model_mod
)
make_htdocs
(in
SloppyCell
)
MichaelisMentenDegradationReaction
Model_mod
(in
SloppyCell
)
make_sens_traj()
(in
SloppyCell.ReactionNetworks.OptDesign
)
MichaelisMentenReaction
my_host
(in
SloppyCell
)
makePermutationMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
minimize_weight_cost()
(in
SloppyCell.ReactionNetworks.OptDesign
)
my_rank
(in
SloppyCell
)
ManyBest()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
misc_c
(in
SloppyCell.setup
)
N
net_ensemble_trajs()
(in
SloppyCell.Ensembles
)
Network_mod
(in
SloppyCell.ReactionNetworks
)
normRows()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
netRadiation()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
new_python_path
(in
SloppyCell.make_htdocs
)
num_procs
(in
SloppyCell
)
Network
normColumns()
(in
SloppyCell.Vandermonde.VdmPairwise
)
O
Observers
(in
SloppyCell
)
OptDesign
(in
SloppyCell.ReactionNetworks
)
OptimizeSumDets
(in
SloppyCell.Vandermonde
)
old_python_path
(in
SloppyCell.make_htdocs
)
Optimization
(in
SloppyCell
)
output_c()
(in
Network
)
OldScipySupport
(in
SloppyCell
)
OptimizeManyTimes()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
P
Parameter
(in
SloppyCell.ReactionNetworks.Components
)
plot_test()
(in
SloppyCell.Subspaces
)
PRAlongP()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
parseTrigger()
(in
Event
)
plot_variance_newpoint()
(in
SloppyCell.ReactionNetworks.OptDesign
)
pretty_plotting()
(in
Network
)
ParticipationRatio()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
plot_variance_newweights()
(in
SloppyCell.ReactionNetworks.OptDesign
)
print_all_costs()
(in
SloppyCell.Observers
)
PCA_eig()
(in
SloppyCell.Ensembles
)
plot_variances()
(in
SloppyCell.ReactionNetworks.OptDesign
)
print_hess_elements()
(in
SloppyCell.Observers
)
PCA_eig_log_params()
(in
SloppyCell.Ensembles
)
plot_variances_log_chems()
(in
SloppyCell.ReactionNetworks.OptDesign
)
PriorInLog
(in
SloppyCell.Residuals
)
PerfectData
(in
SloppyCell.ReactionNetworks
)
plot_variances_subplot()
(in
SloppyCell.ReactionNetworks.OptDesign
)
ProcessFullMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
PeriodCheckResidual
(in
SloppyCell.Residuals
)
plotLevels()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
ProcessHalfMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
plot_eigval_spectrum()
(in
SloppyCell.Plotting
)
Plotting
(in
SloppyCell
)
ProcessQuarterMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
plot_eigvals()
(in
SloppyCell.Plotting
)
Plotting
(in
SloppyCell.ReactionNetworks
)
ProductionReaction
plot_eigvect()
(in
SloppyCell.Plotting
)
pop_item()
(in
KeyedList
)
PromoterReaction
plot_priors()
(in
SloppyCell.Plotting
)
pop_key()
(in
KeyedList
)
Py2TeX
(in
SloppyCell.ExprManip
)
plot_singvals()
(in
SloppyCell.Plotting
)
pop_value()
(in
KeyedList
)
R
Reaction
remove_by_value()
(in
KeyedList
)
Residual
(in
SloppyCell.Residuals
)
ReactionNetworks
(in
SloppyCell
)
remove_component()
(in
Network
)
Residuals
(in
SloppyCell
)
Reactions
(in
SloppyCell.ReactionNetworks
)
res()
(in
Model
)
return_derivs
(in
SloppyCell.ReactionNetworks.Dynamics
)
redchisq()
(in
Model
)
res_dict()
(in
Model
)
reverse()
(in
KeyedList
)
redir
(in
SloppyCell.daskr
)
res_log_params()
(in
Model
)
run_f2py()
(in
Network
)
Redirector
(in
SloppyCell.Redirector_mod
)
reset()
(in
CostEmailer
)
RunInParallel
(in
SloppyCell.ReactionNetworks
)
Redirector_mod
(in
SloppyCell
)
reset()
(in
CostPrinter
)
RunInParallel
(in
SloppyCell
)
reduce_size()
(in
SloppyCell.ReactionNetworks.OptDesign
)
reset_observers()
(in
Model
)
rxn_add_stoich()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
reduce_space
(in
SloppyCell.ReactionNetworks.Dynamics
)
reset_vals_cw()
(in
SloppyCell.Plotting
)
remove_by_key()
(in
KeyedList
)
resetDynamicVariables()
(in
Network
)
S
save()
(in
SloppyCell.Utility
)
set_var_constant()
(in
Network
)
sort_by_key()
(in
KeyedList
)
SBMLInterface
(in
SloppyCell.ReactionNetworks
)
set_var_ic()
(in
Network
)
sort_by_value()
(in
KeyedList
)
SBMLtoDOT()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
set_var_ics()
(in
Network
)
Species
(in
SloppyCell.ReactionNetworks.Components
)
ScaledErrorInFit
(in
SloppyCell.Residuals
)
set_var_optimizable()
(in
Model
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start()
(in
Redirector
)
ScaledExtremum
(in
SloppyCell.Residuals
)
set_var_optimizable()
(in
Network
)
Statement
(in
SloppyCell.RunInParallel
)
SecondOrderReaction
set_var_typical_val()
(in
Network
)
statement_to_all_workers()
(in
SloppyCell.RunInParallel
)
SelfCatalyticMichaelisMentenReaction
set_var_val()
(in
Network
)
STDERR
(in
SloppyCell.Redirector_mod
)
send_email()
(in
SloppyCell.Utility
)
set_var_vals()
(in
Network
)
STDOUT
(in
SloppyCell.Redirector_mod
)
set()
(in
KeyedList
)
SetCalculationCollection()
(in
Model
)
stoichToString()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
set_data()
(in
Experiment
)
setdefault()
(in
KeyedList
)
stop()
(in
Redirector
)
set_deterministic()
(in
Network
)
SetExperimentCollection()
(in
Model
)
stop_workers()
(in
SloppyCell.RunInParallel
)
set_dyn_var_ics()
(in
Network
)
SetName()
(in
Experiment
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subspace_angles()
(in
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)
set_fixed_sf()
(in
Experiment
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setup
(in
SloppyCell
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Subspaces
(in
SloppyCell
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set_ICs()
(in
Model
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(in
SloppyCell.ReactionNetworks.OptDesign
)
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(in
SloppyCell.ExprManip
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set_id()
(in
Network
)
Simplify
(in
SloppyCell.ExprManip
)
sum2Determinants()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_name()
(in
Network
)
single_variance()
(in
SloppyCell.ReactionNetworks.OptDesign
)
sumAllDotProds()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_order()
(in
KeyedList
)
single_variance_change()
(in
SloppyCell.ReactionNetworks.OptDesign
)
sumLogSpacings()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_periodic()
(in
Network
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SloppyCell
sumRowDotProdsNEW()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_sf_prior()
(in
Experiment
)
SloppyCellException
(in
SloppyCell.Utility
)
sumRowDotProdsOLD()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_shared_sf()
(in
Experiment
)
sLSAlongP()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
set_stochastic()
(in
Network
)
solve_lmsys()
(in
SloppyCell.lmopt
)
T
takeDerivative()
(in
Network
)
TINY
(in
SloppyCell.ExprManip.AST
)
Trajectory
(in
SloppyCell.ReactionNetworks.Trajectory_mod
)
TEMP
(in
SloppyCell.make_htdocs
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to_file()
(in
Trajectory
)
Trajectory_mod
(in
SloppyCell.ReactionNetworks
)
test()
(in
SloppyCell.Subspaces
)
to_SBML_l2v1()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
TransformationReaction
test_failure
(in
SloppyCell.make_htdocs
)
toSBMLFile()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
transformMatrix()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
time_slice()
(in
Trajectory
)
toSBMLString()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
TwoProductFirstOrderReaction
timeCostEval()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
traj_ensemble_quantiles()
(in
SloppyCell.Ensembles
)
timeGammas()
(in
SloppyCell.Vandermonde.OptimizeSumDets
)
traj_ensemble_stats()
(in
SloppyCell.Ensembles
)
U
update()
(in
KeyedList
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updateAssignedVars()
(in
Network
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Utility
(in
SloppyCell
)
update_data()
(in
Experiment
)
updateVariablesFromDynamicVars()
(in
Network
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update_optimizable_vars()
(in
Network
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upload_command
(in
SloppyCell.make_htdocs
)
V
vals_cW
(in
SloppyCell.Plotting
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var_change_weighted()
(in
SloppyCell.ReactionNetworks.OptDesign
)
variances()
(in
SloppyCell.ReactionNetworks.OptDesign
)
values()
(in
KeyedList
)
Variable
(in
SloppyCell.ReactionNetworks.Components
)
variances_log_chems()
(in
SloppyCell.ReactionNetworks.OptDesign
)
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(in
SloppyCell
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variance_change()
(in
SloppyCell.ReactionNetworks.OptDesign
)
VdmPairwise
(in
SloppyCell.Vandermonde
)
W
weight_cost()
(in
SloppyCell.ReactionNetworks.OptDesign
)
weights_inv_trans()
(in
SloppyCell.ReactionNetworks.OptDesign
)
weights_trans()
(in
SloppyCell.ReactionNetworks.OptDesign
)
_
__add__()
(in
KeyedList
)
__init__()
(in
TransformationReaction
)
_find_limit_cycle()
(in
Network
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__call__()
(in
CostEmailer
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__init__()
(in
TwoProductFirstOrderReaction
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_get_structure()
(in
Network
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__call__()
(in
CostPrinter
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__init__()
(in
Trajectory
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_get_time_index()
(in
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__copy__()
(in
KeyedList
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__init__()
(in
Redirector
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_hashable_group()
(in
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__deepcopy__()
(in
KeyedList
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__init__()
(in
AmplitudeCheckResidual
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_integral_theorydata()
(in
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__delitem__()
(in
KeyedList
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__init__()
(in
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_integral_theorytheory()
(in
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__delslice__()
(in
KeyedList
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__init__()
(in
PeriodCheckResidual
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_iter_limit_cycle()
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Network
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__deriv_saved
(in
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__init__()
(in
PriorInLog
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_KNOWN_FUNCS
(in
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__eq__()
(in
Event
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__init__()
(in
Residual
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_known_function_bodies
(in
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__eq__()
(in
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__init__()
(in
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_known_structures
(in
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__eq__()
(in
Variable
)
__init__()
(in
ScaledExtremum
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_last_disabled_c
(in
Network
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__eq__()
(in
Reaction
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__init__()
(in
Statement
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_last_structure
(in
Network
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__getitem__()
(in
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__init__()
(in
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(in
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__getstate__()
(in
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__len__()
(in
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_make__assignment()
(in
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__getstate__()
(in
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__mul__()
(in
KeyedList
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_make__sens_assignment()
(in
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__iadd__()
(in
KeyedList
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__ne__()
(in
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_make_alg_deriv_func()
(in
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__imul__()
(in
KeyedList
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__ne__()
(in
FunctionDefinition
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_make_alg_res_func()
(in
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__init__()
(in
CalculationCollection
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__ne__()
(in
Reaction
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_make_ddaskr_jac()
(in
Network
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__init__()
(in
Experiment
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__repr__()
(in
KeyedList
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_make_dres_dc_function()
(in
Network
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__init__()
(in
ExperimentCollection
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__repr__()
(in
Model
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_make_dres_dcdot_function()
(in
Network
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__init__()
(in
KeyedList
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__rmul__()
(in
KeyedList
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_make_dres_dsinglep()
(in
Network
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__init__()
(in
Model
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__setstate__()
(in
Network
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_make_integrate_stochastic_tidbit()
(in
Network
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__init__()
(in
CostEmailer
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__setstate__()
(in
Trajectory
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_make_log_funcs()
(in
Network
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__init__()
(in
CostPrinter
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__str__()
(in
KeyedList
)
_make_res_function()
(in
Network
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__init__()
(in
Bunch
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__str__()
(in
ConstraintViolatedException
)
_make_root_func()
(in
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__init__()
(in
Compartment
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_accept_move()
(in
SloppyCell.Ensembles
)
_make_sens_rhs()
(in
Network
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__init__()
(in
ConstraintEvent
)
_accept_move_recalc_alg()
(in
SloppyCell.Ensembles
)
_makeCrossReferences()
(in
Network
)
__init__()
(in
Event
)
_add_assignments_to_function_body()
(in
Network
)
_makeDiffEqRHS()
(in
Network
)
__init__()
(in
FunctionDefinition
)
_add_variable()
(in
Network
)
_msgs
(in
SloppyCell.daskr
)
__init__()
(in
Parameter
)
_c_module_cache
(in
Network
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_node_attrs
(in
SloppyCell.ExprManip.AST
)
__init__()
(in
Species
)
_checkIdUniqueness()
(in
Network
)
_notify()
(in
Model
)
__init__()
(in
Variable
)
_common_func_strs
(in
Network
)
_ONE
(in
SloppyCell.ExprManip.Differentiation
)
__init__()
(in
Network
)
_common_func_strs_c
(in
Network
)
_ONE
(in
SloppyCell.ExprManip.Simplify
)
__init__()
(in
CoPromoterReaction
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_common_namespace
(in
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)
_OP_ORDER
(in
SloppyCell.ExprManip.AST
)
__init__()
(in
ConstructionReaction
)
_common_namespace
(in
Trajectory
)
_print_sbml_fatals()
(in
SloppyCell.ReactionNetworks.SBMLInterface
)
__init__()
(in
ExponentialDecayReaction
)
_common_prototypes_c
(in
Network
)
_py_func_dict_cache
(in
Network
)
__init__()
(in
FirstOrderReaction
)
_compute_sf_and_sfent_for_expt()
(in
Model
)
_quadratic_cost()
(in
SloppyCell.Ensembles
)
__init__()
(in
HeterodimerDissociationReaction
)
_double_epsilon_
(in
SloppyCell.Model_mod
)
_sampling_matrix()
(in
SloppyCell.Ensembles
)
__init__()
(in
HeterodimerizationReaction
)
_double_epsilon_
(in
SloppyCell.ReactionNetworks.Dynamics
)
_save_ens()
(in
SloppyCell.Ensembles
)
__init__()
(in
HillDegradationReaction
)
_double_max_
(in
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)
_sens_event_derivs_cache
(in
Network
)
__init__()
(in
HillTransportReaction
)
_double_tiny_
(in
SloppyCell.ReactionNetworks.Dynamics
)
_smooth_trigger()
(in
Network
)
__init__()
(in
HomodimerDissociationReaction
)
_double_tiny_
(in
SloppyCell.ReactionNetworks.Network_mod
)
_standard_func_defs
(in
Network
)
__init__()
(in
HomodimerizationReaction
)
_dynamic_event_methods
(in
Network
)
_sub_for_piecewise()
(in
Network
)
__init__()
(in
MichaelisMentenDegradationReaction
)
_dynamic_funcs
(in
Trajectory
)
_sub_for_piecewise_ast()
(in
Network
)
__init__()
(in
MichaelisMentenReaction
)
_dynamic_structure_methods
(in
Network
)
_sub_var_names()
(in
Trajectory
)
__init__()
(in
ProductionReaction
)
_eliminate_slowest_mode()
(in
Network
)
_TEMP_DIR
(in
SloppyCell
)
__init__()
(in
PromoterReaction
)
_EMPTY_MUL
(in
SloppyCell.ExprManip.Py2TeX
)
_trial_move()
(in
SloppyCell.Ensembles
)
__init__()
(in
Reaction
)
_epsilon
(in
SloppyCell.lmopt
)
_VERSION
(in
SloppyCell
)
__init__()
(in
SecondOrderReaction
)
_evaluate()
(in
Model
)
_ZERO
(in
SloppyCell.ExprManip.Differentiation
)
__init__()
(in
SelfCatalyticMichaelisMentenReaction
)
_FARTHEST_OUT
(in
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)
_ZERO
(in
SloppyCell.ExprManip.Simplify
)
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