Index

_

__init__() (pudu.assembly.BaseAssembly method) (pudu.assembly.Domestication method) (pudu.assembly.ManualAssembly method) (pudu.assembly.ManualLoopAssembly method) (pudu.assembly.SBOLLoopAssembly method) (pudu.calibration.BaseCalibration method) (pudu.plating.ManualPlating method) (pudu.plating.Plating method) (pudu.sample_preparation.PlateSamples method) (pudu.sample_preparation.PlateWithGradient method) (pudu.sample_preparation.SamplePreparation method) (pudu.transformation.HeatShockTransformation method) (pudu.transformation.ManualTransformation method) (pudu.transformation.Transformation method) (pudu.utils.Camera method) (pudu.utils.SmartPipette method)

B

backbone_name (pudu.assembly.ManualReactionRecord attribute) backbone_uri (pudu.assembly.ManualReactionRecord attribute) bacterium_locations (pudu.plating.Plating attribute)

BaseAssembly (class in pudu.assembly) BaseCalibration (class in pudu.calibration) build_agar_plate_map() (pudu.plating.Plating method)

C

calculate_plate_layout() (pudu.plating.Plating method) Camera (class in pudu.utils) capture_picture() (pudu.utils.Camera method) chassis_name (pudu.transformation.ManualTransformationRecord attribute)

chassis_uri (pudu.transformation.ManualTransformationRecord attribute) cleanup_ffmpeg_processes() (pudu.utils.Camera method) colors (in module pudu.utils) construct_name (pudu.plating.ManualPlatingRecord attribute)

D

detect_protocol_type() (in module pudu.generate_protocol)

dilution_factor (pudu.plating.Plating attribute) Domestication (class in pudu.assembly)

F

fixed_reagent_volume (pudu.assembly.ManualReactionRecord attribute)

format_python_value() (in module pudu.generate_protocol)

G

generate_param_reference() (in module pudu.generate_protocol) generate_protocol() (in module pudu.generate_protocol) get_aspiration_location() (pudu.utils.SmartPipette method) get_conical_tube_aspiration_height() (pudu.utils.SmartPipette method)

get_plates_json() (pudu.plating.Plating method) get_well_height() (pudu.utils.SmartPipette method) get_well_volume() (pudu.utils.SmartPipette method) get_xlsx_output() (pudu.assembly.BaseAssembly method) GFPODCalibration (class in pudu.calibration)

H

HeatShockTransformation (class in pudu.transformation)

I

is_conical_tube() (pudu.utils.SmartPipette method)

L

liquid_transfer() (pudu.assembly.BaseAssembly method) (pudu.transformation.HeatShockTransformation method) (pudu.utils.SmartPipette method)

LoopAssembly (class in pudu.assembly)

M

main() (in module pudu.generate_protocol) ManualAssembly (class in pudu.assembly) ManualLoopAssembly (class in pudu.assembly) ManualPlating (class in pudu.plating) ManualPlatingRecord (class in pudu.plating)

ManualReactionRecord (class in pudu.assembly) ManualTransformation (class in pudu.transformation) ManualTransformationRecord (class in pudu.transformation) max_colonies (pudu.plating.Plating attribute) module pudu.generate_protocol

N

notes (pudu.assembly.ManualReactionRecord attribute) number_constructs (pudu.plating.Plating attribute)

number_dilutions (pudu.plating.Plating attribute) number_of_dna_components (pudu.assembly.ManualReactionRecord attribute)

P

part_names (pudu.assembly.ManualReactionRecord attribute) part_uris (pudu.assembly.ManualReactionRecord attribute) plasmid_names (pudu.transformation.ManualTransformationRecord attribute) plasmid_uris (pudu.transformation.ManualTransformationRecord attribute) PlateSamples (class in pudu.sample_preparation) PlateWithGradient (class in pudu.sample_preparation) Plating (class in pudu.plating) process_assemblies() (pudu.assembly.BaseAssembly method) (pudu.assembly.Domestication method) (pudu.assembly.ManualAssembly method) (pudu.assembly.ManualLoopAssembly method) (pudu.assembly.SBOLLoopAssembly method)

process_bacterium_locations() (pudu.plating.ManualPlating method) process_transformations() (pudu.transformation.ManualTransformation method) product_name (pudu.assembly.ManualReactionRecord attribute) product_uri (pudu.assembly.ManualReactionRecord attribute) protocol_name (pudu.plating.Plating attribute) pudu.generate_protocol module

R

reagent_additions (pudu.assembly.ManualReactionRecord attribute) render_markdown() (pudu.assembly.ManualAssembly method) (pudu.plating.ManualPlating method) (pudu.transformation.ManualTransformation method) replicates (pudu.plating.Plating attribute) restriction_enzyme_name (pudu.assembly.ManualReactionRecord attribute) restriction_enzyme_uri (pudu.assembly.ManualReactionRecord attribute)

RGBODCalibration (class in pudu.calibration) run() (pudu.assembly.BaseAssembly method) (pudu.calibration.BaseCalibration method) (pudu.plating.Plating method) (pudu.sample_preparation.PlateSamples method) (pudu.sample_preparation.PlateWithGradient method) (pudu.sample_preparation.SamplePreparation method) (pudu.transformation.HeatShockTransformation method)

S

SamplePreparation (class in pudu.sample_preparation) SBOLLoopAssembly (class in pudu.assembly) setup_tip_management() (pudu.assembly.BaseAssembly method) SmartPipette (class in pudu.utils)

source_well (pudu.plating.ManualPlatingRecord attribute) start_video() (pudu.utils.Camera method) stop_video() (pudu.utils.Camera method) strain_name (pudu.transformation.ManualTransformationRecord attribute) strain_uri (pudu.transformation.ManualTransformationRecord attribute)

T

total_colonies (pudu.plating.Plating attribute) total_dna_volume (pudu.assembly.ManualReactionRecord attribute)

total_reaction_volume (pudu.assembly.ManualReactionRecord attribute) Transformation (class in pudu.transformation)

V

volume_bacteria_transfer (pudu.plating.Plating attribute) volume_colony (pudu.plating.Plating attribute)

volume_lb (pudu.plating.Plating attribute) volume_total_reaction (pudu.plating.Plating attribute)

W

water_volume (pudu.assembly.ManualReactionRecord attribute) write_markdown() (pudu.assembly.ManualAssembly method) (pudu.plating.ManualPlating method) (pudu.transformation.ManualTransformation method)

write_plates_excel() (pudu.plating.Plating method) write_plates_json() (pudu.plating.Plating method)