Index

A

add_annotations() (in module constrain.lims.csv_database) add_content() (constrain.lab.containers_wells_picklists.Well method) add_sequences_to_dataframe() (in module constrain.lims.csv_database) add_transfer() (constrain.lab.containers_wells_picklists.PickList method)

add_unique_ids() (in module constrain.lims.csv_database) amplicon_by_name() (in module constrain.lab.PCR) apply() (constrain.lab.containers_wells_picklists.Transfer method) assembly_maker() (in module constrain.design.combinatorial_design)

C

calculate_elongation_time() (in module constrain.lab.PCR) calculate_processing_speed() (in module constrain.lab.PCR) calculate_required_thermal_cyclers() (in module constrain.lab.PCR) calculate_volume_and_total_concentration() (in module constrain.lab.transformation) calculate_volumes() (in module constrain.lab.PCR) capacity (constrain.lab.containers_wells_picklists.Well attribute) CAS9_cutting() (in module constrain.design.cloning) casembler() (in module constrain.design.cloning) change_row() (in module constrain.lims.csv_database) combinatorial_list_maker() (in module constrain.design.combinatorial_design) components_as_string() (constrain.lab.containers_wells_picklists.WellContent method) compute_rows_columns() (in module constrain.lab.containers_wells_picklists) concatenating_list_of_dfs() (in module constrain.test.genotyping) concentration() (constrain.lab.containers_wells_picklists.WellContent method) constrain module constrain.design module constrain.design.cloning module, [1] constrain.design.combinatorial_design module, [1] constrain.design.fetch_sequences module constrain.design.teselagen_helpers module constrain.lab module

constrain.lab.containers_wells_picklists module, [1] constrain.lab.PCR module, [1] constrain.lab.robot_assembly module, [1] constrain.lab.transformation module, [1] constrain.lims module constrain.lims.benchling_api module, [1] constrain.lims.csv_database module, [1] constrain.machine_learning module constrain.plotting module constrain.test module constrain.test.genotyping module, [1] constrain.utils module coordinates (constrain.lab.containers_wells_picklists.Well property) coordinates_to_wellname() (in module constrain.lab.containers_wells_picklists) count_unique_parts() (in module constrain.design.combinatorial_design) CRIPSR_knockout() (in module constrain.design.cloning)

D

dead_volume_per_transfer_class (constrain.lab.containers_wells_picklists.Well attribute)

delete_row_df() (in module constrain.lims.csv_database) DesignAssembly (class in constrain.design.combinatorial_design)

E

empty_completely() (constrain.lab.containers_wells_picklists.Well method) empty_list_maker() (in module constrain.design.combinatorial_design) enforce_maximum_dispense_volume() (constrain.lab.containers_wells_picklists.PickList method)

extract_gRNAs() (in module constrain.design.cloning) extract_sites() (in module constrain.design.cloning) extract_template_amplification_sites() (in module constrain.design.cloning)

F

find_unique_well_by_condition() (constrain.lab.containers_wells_picklists.Plate method) find_unique_well_containing() (constrain.lab.containers_wells_picklists.Plate method)

FlowbotInstructionsToCSV() (constrain.lab.robot_assembly.RobotAssembly method) from_benchling() (in module constrain.lims.benchling_api)

G

get_box() (in module constrain.lims.csv_database) get_database() (in module constrain.lims.csv_database) get_dna_from_box_name() (in module constrain.lims.csv_database) get_dna_from_plate_name() (in module constrain.lims.csv_database) get_plate() (in module constrain.lims.csv_database)

get_primers() (in module constrain.design.combinatorial_design) get_unique_id() (in module constrain.lims.csv_database) get_well_at_index() (constrain.lab.containers_wells_picklists.Plate method) graphical_representation_of_assemblies() (constrain.design.combinatorial_design.DesignAssembly method) grouper() (in module constrain.lab.PCR)

I

index_in_plate() (constrain.lab.containers_wells_picklists.Well method) index_to_row_column() (in module constrain.lab.containers_wells_picklists) index_to_wellname() (constrain.lab.containers_wells_picklists.Plate method) (in module constrain.lab.containers_wells_picklists)

is_after() (constrain.lab.containers_wells_picklists.Well method) is_empty (constrain.lab.containers_wells_picklists.Well property) iter_wells() (constrain.lab.containers_wells_picklists.Plate method) iterate_sources_tree() (constrain.lab.containers_wells_picklists.Well method)

L

LiquidHandler (class in constrain.lab.robot_assembly) list_filtered_wells() (constrain.lab.containers_wells_picklists.Plate method)

list_well_data_fields() (constrain.lab.containers_wells_picklists.Plate method) list_wells_in_column() (constrain.lab.containers_wells_picklists.Plate method) list_wells_in_row() (constrain.lab.containers_wells_picklists.Plate method)

M

make_empty() (constrain.lab.containers_wells_picklists.WellContent method) make_virtual_plates_fromDF() (in module constrain.lab.robot_assembly) making_assembled_contigs() (in module constrain.design.combinatorial_design) making_assembly_objects() (in module constrain.design.combinatorial_design) merge_picklists() (constrain.lab.containers_wells_picklists.PickList static method) module constrain constrain.design constrain.design.cloning, [1] constrain.design.combinatorial_design, [1] constrain.design.fetch_sequences constrain.design.teselagen_helpers constrain.lab constrain.lab.containers_wells_picklists, [1] constrain.lab.PCR, [1] constrain.lab.robot_assembly, [1] constrain.lab.transformation, [1] constrain.lims constrain.lims.benchling_api, [1] constrain.lims.csv_database, [1] constrain.machine_learning constrain.plotting constrain.test constrain.test.genotyping, [1] constrain.utils

multiply_list() (in module constrain.design.cloning)

N

nanophotometer_concentrations() (in module constrain.lab.PCR) ng_to_nmol() (in module constrain.lab.transformation) nicking_enzyme() (in module constrain.design.cloning) NoUniqueWell

num_columns (constrain.lab.containers_wells_picklists.Plate2x4 attribute) (constrain.lab.containers_wells_picklists.Plate96 attribute) num_rows (constrain.lab.containers_wells_picklists.Plate2x4 attribute) (constrain.lab.containers_wells_picklists.Plate96 attribute) number_to_rowname() (in module constrain.lab.containers_wells_picklists)

O

ODtime() (in module constrain.lab.transformation)

P

pairwise_alignment_of_templates() (in module constrain.test.genotyping) PCR_list() (constrain.design.combinatorial_design.DesignAssembly method) PCR_list_to_dataframe() (constrain.design.combinatorial_design.DesignAssembly method) pcr_locations() (in module constrain.lab.PCR) PickList (class in constrain.lab.containers_wells_picklists) picklist_from_plates() (in module constrain.lab.robot_assembly) plat_seq_data_wrangler() (in module constrain.test.genotyping) Plate (class in constrain.lab.containers_wells_picklists) Plate2x4 (class in constrain.lab.containers_wells_picklists) Plate96 (class in constrain.lab.containers_wells_picklists) plate_AvgQual() (in module constrain.test.genotyping)

plate_plot() (in module constrain.design.cloning) PlatesToExcelFile() (constrain.lab.robot_assembly.RobotAssembly method) pool_parts() (in module constrain.lab.transformation) pretty_summary() (constrain.lab.containers_wells_picklists.Well method) primer_list() (constrain.design.combinatorial_design.DesignAssembly method) primer_list_to_dataframe() (constrain.design.combinatorial_design.DesignAssembly method) primer_ta_neb() (in module constrain.lab.PCR) primer_tm_neb() (in module constrain.lab.PCR) print_PCR_list() (constrain.design.combinatorial_design.DesignAssembly method) print_pooled_parts() (in module constrain.lab.transformation) print_primer_list() (constrain.design.combinatorial_design.DesignAssembly method) print_well_df_to_string() (constrain.lab.robot_assembly.RobotAssembly method)

Q

Q5_NEB_PCR_program() (in module constrain.lab.PCR)

R

recs_no_duplicates() (in module constrain.design.cloning) recs_no_duplicates_names() (in module constrain.design.cloning) remove_features_with_negative_loc() (in module constrain.design.cloning) remove_tuple_duplicates() (in module constrain.design.cloning) replace_nans_in_dict() (in module constrain.lab.containers_wells_picklists)

restricted_to() (constrain.lab.containers_wells_picklists.PickList method) return_column() (constrain.lab.containers_wells_picklists.Plate method) return_row() (constrain.lab.containers_wells_picklists.Plate method) RobotAssembly (class in constrain.lab.robot_assembly) rowname_to_number() (in module constrain.lab.containers_wells_picklists)

S

seq_to_annotation() (in module constrain.design.cloning) sequence_to_benchling() (in module constrain.lims.benchling_api) session (in module constrain.lims.benchling_api) set_plate_locations() (in module constrain.lab.PCR) ShowContigs() (constrain.design.combinatorial_design.DesignAssembly method) ShowVariantsLibDF() (constrain.design.combinatorial_design.DesignAssembly method)

simple_amplicon_maker() (in module constrain.design.combinatorial_design) simulate() (constrain.lab.containers_wells_picklists.PickList method) slicing_and_naming_seq_plates() (in module constrain.test.genotyping) sorted_by() (constrain.lab.containers_wells_picklists.PickList method) split_df_names() (in module constrain.test.genotyping) subtract_content() (constrain.lab.containers_wells_picklists.Well method) systematic_names_function() (in module constrain.design.combinatorial_design)

T

time_to_inculate() (in module constrain.lab.transformation) to_dict() (constrain.lab.containers_wells_picklists.Plate method) (constrain.lab.containers_wells_picklists.Well method) (constrain.lab.containers_wells_picklists.WellContent method) to_flowbot_instructions() (constrain.lab.containers_wells_picklists.Transfer method) (constrain.lab.robot_assembly.LiquidHandler method) to_flowbot_instructions_string() (constrain.lab.containers_wells_picklists.PickList method) to_pandas_dataframe() (constrain.lab.containers_wells_picklists.Plate method)

to_plain_string() (constrain.lab.containers_wells_picklists.PickList method) (constrain.lab.containers_wells_picklists.Transfer method) to_plain_textfile() (constrain.lab.containers_wells_picklists.PickList method) to_short_string() (constrain.lab.containers_wells_picklists.Transfer method) total_transferred_volume() (constrain.lab.containers_wells_picklists.PickList method) Transfer (class in constrain.lab.containers_wells_picklists) TransferError transformation_mix() (in module constrain.lab.transformation) transformation_partitipants() (in module constrain.lab.transformation)

U

unique_amplicons() (in module constrain.design.combinatorial_design) unique_primers() (in module constrain.design.combinatorial_design) UPandDW() (in module constrain.design.cloning)

update_amplicon_annotations() (in module constrain.lab.PCR) update_database() (in module constrain.lims.csv_database) update_loc_vol_conc() (in module constrain.lims.benchling_api) USER_enzyme() (in module constrain.design.cloning)

V

volume (constrain.lab.containers_wells_picklists.Well property)

W

wanted_mass() (in module constrain.lab.transformation) wanted_volume() (in module constrain.lab.transformation) Well (class in constrain.lab.containers_wells_picklists) well_class (constrain.lab.containers_wells_picklists.Plate attribute) well_keys_96() (in module constrain.lab.robot_assembly) WellContent (class in constrain.lab.containers_wells_picklists)

wellname_to_coordinates() (in module constrain.lab.containers_wells_picklists) wellname_to_index() (constrain.lab.containers_wells_picklists.Plate method) (in module constrain.lab.containers_wells_picklists) wells_grouped_by() (constrain.lab.containers_wells_picklists.Plate method) wells_sorted_by() (constrain.lab.containers_wells_picklists.Plate method) with_new_volume() (constrain.lab.containers_wells_picklists.Transfer method)