impact
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impact
Impact: a framework for analyzing microbial physiology
Install
Documentation
Quickstart
Importing data
Querying and filtering for data
Visualization
Exploring features
Core structure
TrialIdentifier
class
AnalyteData
SingleTrial
ReplicateTrial
Experiment
Project
Analyzing Features
Rates
Specific Productivity
Metabolic Model Integration
dFBA Batch Integration
Carbon Balance
Flux mapping with escher
Stages
Adding custom functionality
Writing a new parser
impact package
Subpackages
Submodules
Module contents
This page
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
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P
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R
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S
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T
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U
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V
A
add_analyte_data() (impact.core.features.BaseAnalyteFeatureFactory method)
(impact.core.SingleTrial.SingleTrial method)
(impact.core.features.NormalizedDataFactory method)
(impact.core.features.ODNormalizedDataFactory method)
(impact.core.features.ProductYieldFactory method)
(impact.core.features.SpecificProductivityFactory method)
add_experiment() (impact.core.Project.Project method)
add_replicate() (impact.core.ReplicateTrial.ReplicateTrial method)
add_replicate_trial() (impact.core.Experiment.Experiment method)
add_timepoint() (impact.core.AnalyteData.EndPoint method)
(impact.core.AnalyteData.TimeCourse method)
add_user() (impact.core.Project.Project method)
add_user_permission() (impact.core.Project.Project method)
analyte_dict (impact.core.SingleTrial.SingleTrial attribute)
analyte_name (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
analyte_names (impact.core.Experiment.Experiment attribute)
analyte_type (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
analyte_types (impact.core.SingleTrial.SingleTrial attribute)
avg (impact.core.ReplicateTrial.ReplicateTrial attribute)
avg_id (impact.core.ReplicateTrial.ReplicateTrial attribute)
B
bad_replicates (impact.core.ReplicateTrial.ReplicateTrial attribute)
BaseAnalyteFeature (class in impact.core.features)
BaseAnalyteFeatureFactory (class in impact.core.features)
bind_engine() (in module impact.database)
Biomass (class in impact.core.AnalyteData)
blank (impact.core.ReplicateTrial.ReplicateTrial attribute)
blank_id (impact.core.ReplicateTrial.ReplicateTrial attribute)
C
calcFit() (impact.curve_fitting.core.CurveFitObject method)
calculate() (impact.core.AnalyteData.TimeCourse method)
(impact.core.Experiment.Experiment method)
(impact.core.ReplicateTrial.ReplicateTrial method)
(impact.core.SingleTrial.SingleTrial method)
(impact.core.features.COBRAModelFactory method)
(impact.core.features.MassBalance method)
(impact.core.features.ODNormalizedData method)
(impact.core.features.ProductYield method)
(impact.core.features.SpecificProductivity method)
calculate_mass_balance() (impact.core.SingleTrial.SingleTrial method)
calculate_ODE_fit() (impact.core.SingleTrial.SingleTrial method)
calculate_statistics() (impact.core.ReplicateTrial.ReplicateTrial method)
calculate_substrate_consumed() (impact.core.features.MassBalance method)
(impact.core.features.ProductYield method)
calculations_uptodate (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
check_replicate_unique_id_match() (impact.core.ReplicateTrial.ReplicateTrial method)
class_features (impact.core.SingleTrial.SingleTrial attribute)
COBRAModelFactory (class in impact.core.features)
colorMap (impact.core.Project.Project attribute)
create_db() (in module impact.database)
create_session() (in module impact.database)
create_stage() (impact.core.AnalyteData.TimeCourse method)
(impact.core.ReplicateTrial.ReplicateTrial method)
(impact.core.SingleTrial.SingleTrial method)
curve_fit_data() (impact.core.AnalyteData.Biomass method)
(impact.core.AnalyteData.Product method)
(impact.core.AnalyteData.Reporter method)
(impact.core.AnalyteData.Substrate method)
(impact.core.AnalyteData.TimeCourse method)
curve_fit_dict (in module impact.curve_fitting.methods)
CurveFitObject (class in impact.curve_fitting.core)
D
data (impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.features.BaseAnalyteFeature attribute)
(impact.core.features.MassBalance attribute)
(impact.core.features.NormalizedData attribute)
(impact.core.features.ODNormalizedData attribute)
(impact.core.features.ProductYield attribute)
(impact.core.features.SpecificProductivity attribute)
data() (impact.core.Experiment.Experiment method)
data_curve_fit() (impact.core.AnalyteData.TimeCourse method)
data_vector (impact.core.AnalyteData.TimeCourse attribute)
db_name (impact.core.settings.Settings attribute)
default_outlier_cleaning_flag (impact.core.settings.Settings attribute)
delete_user() (impact.core.Project.Project method)
discriminator (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
dynamic_model_integration() (in module impact.helpers.synthetic_data)
E
end_date (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
end_time (impact.core.Experiment.Stage attribute)
EndPoint (class in impact.core.AnalyteData)
Experiment (class in impact.core.Experiment)
F
find_death_phase() (impact.core.AnalyteData.TimeCourse method)
find_death_phase_static() (impact.core.AnalyteData.TimeCourse static method)
fit_params (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
fit_type (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
FitParameter (class in impact.core.AnalyteData)
G
generalized_logistic() (in module impact.curve_fitting.methods)
generate_data() (in module impact.helpers.synthetic_data)
generate_replicate_trial() (in module impact.helpers.synthetic_data)
generate_time_point_list() (impact.core.AnalyteData.TimeCourse method)
generic_timecourse() (in module impact.plotting)
get_analytes() (impact.core.ReplicateTrial.ReplicateTrial method)
get_colors() (in module impact.plotting)
get_experiment() (impact.core.Project.Project method)
get_growth_rate() (impact.curve_fitting.core.GrowthRateSplineExtraction method)
get_normalized_data() (impact.core.ReplicateTrial.ReplicateTrial method)
get_unique_analytes() (impact.core.ReplicateTrial.ReplicateTrial method)
get_unique_timepoint_id() (impact.core.AnalyteData.TimePoint method)
gompertz() (in module impact.curve_fitting.methods)
gradient (impact.core.AnalyteData.TimeCourse attribute)
gradient_points (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
GradientTimePoint (class in impact.core.AnalyteData)
GrowthRateSplineExtraction (class in impact.curve_fitting.core)
H
HPLC_titer_parser() (in module impact.parsers)
I
id (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.FitParameter attribute)
(impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
(impact.core.settings.Settings attribute)
Identifier (class in impact.core.Project)
impact (module)
impact.api (module)
impact.core (module)
impact.core.AnalyteData (module)
impact.core.Experiment (module)
impact.core.features (module)
impact.core.Project (module)
impact.core.ReplicateTrial (module)
impact.core.secrets (module)
impact.core.settings (module)
impact.core.SingleTrial (module)
impact.curve_fitting (module)
impact.curve_fitting.core (module)
impact.curve_fitting.methods (module)
impact.custom_parsers (module)
impact.database (module)
impact.helpers (module)
impact.helpers.synthetic_data (module)
impact.parsers (module)
impact.plotting (module)
import_date (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
J
janoschek() (in module impact.curve_fitting.methods)
L
link_identifiers() (impact.core.ReplicateTrial.ReplicateTrial method)
(impact.core.SingleTrial.SingleTrial method)
live_calculations (impact.core.settings.Settings attribute)
M
MassBalance (class in impact.core.features)
MassBalanceFactory (class in impact.core.features)
max_fraction_replicates_to_remove (impact.core.settings.Settings attribute)
minimum_points_for_curve_fit (impact.core.settings.Settings attribute)
N
name (impact.core.features.BaseAnalyteFeatureFactory attribute)
(impact.core.features.NormalizedDataFactory attribute)
(impact.core.features.ODNormalizedDataFactory attribute)
(impact.core.features.ProductYieldFactory attribute)
(impact.core.features.SpecificProductivityFactory attribute)
normalize_data() (impact.core.SingleTrial.SingleTrial method)
NormalizedData (class in impact.core.features)
NormalizedDataFactory (class in impact.core.features)
notes (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
O
ODNormalizedData (class in impact.core.features)
ODNormalizedDataFactory (class in impact.core.features)
order_preserve_sort() (in module impact.plotting)
outlier_cleaning_flag (impact.core.settings.Settings attribute)
P
Parameter (class in impact.curve_fitting.methods)
parameter_name (impact.core.AnalyteData.FitParameter attribute)
parameter_value (impact.core.AnalyteData.FitParameter attribute)
parent (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.Experiment.Stage attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
parent_id (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.FitParameter attribute)
(impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.Experiment.Stage attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
parse_analyte_data() (in module impact.parsers)
parse_raw_data() (impact.core.Experiment.Experiment method)
(impact.parsers.Parser class method)
(in module impact.parsers)
parse_raw_identifier() (in module impact.parsers)
parse_single_trial_list() (in module impact.parsers)
parse_time_point_list() (in module impact.parsers)
Parser (class in impact.parsers)
parser_case_dict (impact.parsers.Parser attribute)
perform_curve_fit (impact.core.settings.Settings attribute)
print_generic_timecourse_plotly() (in module impact.plotting)
printGenericTimeCourse_plotly() (in module impact.plotting)
Product (class in impact.core.AnalyteData)
ProductYield (class in impact.core.features)
ProductYieldFactory (class in impact.core.features)
Project (class in impact.core.Project)
prune_bad_replicates() (impact.core.ReplicateTrial.ReplicateTrial method)
R
register_feature() (impact.core.SingleTrial.SingleTrial class method)
register_parser() (impact.parsers.Parser class method)
remove_death_phase_flag (impact.core.settings.Settings attribute)
render_output_ploty() (in module impact.plotting)
replicate_ids (impact.core.ReplicateTrial.ReplicateTrial attribute)
replicate_trial_dict (impact.core.Experiment.Experiment attribute)
replicate_trials (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
ReplicateTrial (class in impact.core.ReplicateTrial)
Reporter (class in impact.core.AnalyteData)
requires (impact.core.features.BaseAnalyteFeatureFactory attribute)
(impact.core.features.NormalizedDataFactory attribute)
(impact.core.features.ODNormalizedDataFactory attribute)
(impact.core.features.ProductYieldFactory attribute)
(impact.core.features.SpecificProductivityFactory attribute)
richard_5() (in module impact.curve_fitting.methods)
S
savgolFilterWindowSize (impact.core.settings.Settings attribute)
scientist_1 (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
scientist_2 (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
serialize() (impact.core.AnalyteData.TimeCourse method)
(impact.core.SingleTrial.SingleTrial method)
set_blank() (impact.core.ReplicateTrial.ReplicateTrial method)
set_blanks() (impact.core.Experiment.Experiment method)
set_stages() (impact.core.Experiment.Experiment method)
Settings (class in impact.core.settings)
single_trial_dict (impact.core.ReplicateTrial.ReplicateTrial attribute)
single_trials (impact.core.ReplicateTrial.ReplicateTrial attribute)
SingleTrial (class in impact.core.SingleTrial)
specific_productivity_points (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
SpecificProductivity (class in impact.core.features)
SpecificProductivityFactory (class in impact.core.features)
SpecificProductivityTimePoint (class in impact.core.AnalyteData)
spectromax_OD() (in module impact.parsers)
spectromax_OD_triplicate() (in module impact.parsers)
Stage (class in impact.core.Experiment)
stage_id (impact.core.Experiment.Stage attribute)
stage_indices (impact.core.AnalyteData.TimeCourse attribute)
(impact.core.SingleTrial.SingleTrial attribute)
stage_parent (impact.core.AnalyteData.TimeCourseStage attribute)
stage_parent_id (impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
stages (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
start_date (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
start_time (impact.core.Experiment.Stage attribute)
std (impact.core.ReplicateTrial.ReplicateTrial attribute)
std_id (impact.core.ReplicateTrial.ReplicateTrial attribute)
strains (impact.core.Experiment.Experiment attribute)
substract_blank() (impact.core.ReplicateTrial.ReplicateTrial method)
Substrate (class in impact.core.AnalyteData)
summary() (impact.core.Experiment.Experiment method)
(impact.core.SingleTrial.SingleTrial method)
svg_plot() (in module impact.plotting)
T
tecan_OD() (in module impact.parsers)
three_param_growth() (in module impact.curve_fitting.methods)
time (impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.TimePoint attribute)
time_point_type (impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.TimePoint attribute)
time_points (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
time_profile_traces() (in module impact.plotting)
time_profile_traces_single_trials() (in module impact.plotting)
time_vector (impact.core.AnalyteData.TimeCourse attribute)
TimeCourse (class in impact.core.AnalyteData)
TimeCourseStage (class in impact.core.AnalyteData)
TimePoint (class in impact.core.AnalyteData)
title (impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
trial_identifier (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
trial_identifier_id (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.AnalyteData.TimePoint attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
(impact.core.SingleTrial.SingleTrial attribute)
type (impact.core.AnalyteData.Biomass attribute)
(impact.core.AnalyteData.EndPoint attribute)
(impact.core.AnalyteData.Product attribute)
(impact.core.AnalyteData.Reporter attribute)
(impact.core.AnalyteData.Substrate attribute)
(impact.core.AnalyteData.TimeCourse attribute)
(impact.core.AnalyteData.TimeCourseStage attribute)
(impact.core.Experiment.Experiment attribute)
(impact.core.Experiment.Stage attribute)
U
unique_id (impact.core.AnalyteData.TimeCourse attribute)
(impact.core.ReplicateTrial.ReplicateTrial attribute)
use_filtered_data (impact.core.settings.Settings attribute)
use_in_analysis (impact.core.AnalyteData.GradientTimePoint attribute)
(impact.core.AnalyteData.SpecificProductivityTimePoint attribute)
(impact.core.AnalyteData.TimePoint attribute)
V
verbose (impact.core.settings.Settings attribute)