impact.core.Experiment.Experiment(**kwargs)¶Bases: sqlalchemy.ext.declarative.api.Base
Attributes
analyte_names |
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replicate_trial_dict |
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strains |
Methods
add_replicate_trial(replicateTrial) |
Add a ReplicateTrial to the experiment. |
calculate() |
|
data() |
|
parse_raw_data(*args, **kwargs) |
Wrapper for parsing data into an experiment |
set_blanks([mode]) |
Define how to associate blanks and perform blank subtraction. |
set_stages([stage_indices]) |
Set the stages for the experiment. |
summary([level]) |
add_replicate_trial(replicateTrial)¶Add a ReplicateTrial to the experiment.
| Parameters: | replicateTrial : ReplicateTrial |
|---|
analyte_names¶calculate()¶data()¶end_date¶id¶import_date¶notes¶parse_raw_data(*args, **kwargs)¶Wrapper for parsing data into an experiment
| Parameters: | args kwargs |
|---|
replicate_trial_dict¶replicate_trials¶scientist_1¶scientist_2¶set_blanks(mode='auto')¶Define how to associate blanks and perform blank subtraction. Parameters ———- mode (str) : how to determine blanks common_id (str) : which identifier to use
NEW BLANKS DEFINITION. Previously, a ‘common_id’ was used as an identifier to figure out blanks for each replicate Blanks only need to be media dependent. This definition of blanks assigns a blank to a replicate trial if the media are the same. If not, it calculates the number of common components and assigns the blank with the most number of common components to that particular media. It is however good practice to have blanks for each media used.
set_stages(stage_indices=None)¶Set the stages for the experiment. These stages can be defined manually based on growth kinetics or batch condition changes such as inducer additions.
| Parameters: | stage_times —–> Removed because indices in pandas are the time values stage_indices |
|---|
stages¶start_date¶strains¶summary(level=None)¶title¶type¶impact.core.Experiment.Stage(**kwargs)¶Bases: impact.core.Experiment.Experiment
Attributes
analyte_names |
|
replicate_trial_dict |
|
strains |
Methods
add_replicate_trial(replicateTrial) |
Add a ReplicateTrial to the experiment. |
calculate() |
|
data() |
|
parse_raw_data(*args, **kwargs) |
Wrapper for parsing data into an experiment |
set_blanks([mode]) |
Define how to associate blanks and perform blank subtraction. |
set_stages([stage_indices]) |
Set the stages for the experiment. |
summary([level]) |
end_date¶end_time¶id¶import_date¶notes¶parent¶parent_id¶replicate_trials¶scientist_1¶scientist_2¶stage_id¶stages¶start_date¶start_time¶title¶type¶