[Beta] Procedures

Definitions

TermDefinition
ProcedureA template for the recipe or assay. Lives in a template collection.
MethodUnit operation
ParameterMaterial input, material output, equipment, or parameter. The parameter_type column disambiguates between the four. Data parameters are just referred to as "parameters" in the UI.
Parameter LibraryLibrary of configurable parameters that can be used within a procedure.
Procedure run plan

Recipe Run Plans (for Process Development Studies) and Assay Run Plans (for Assay-based Studies) are both saved as Procedure run plans in the warehouse.

This is essentially a draft procedure run. It becomes a procedure run (Recipe Run or Assay Run) once promoted.

Process flowchart config versionThe ID of the specific version of the Recipe or Assay that will be used for this planned run (or was used in the case of a promoted run plan)

Table Overviews

Name$raw FiltersDescription
bnch$procedure_run$betaarchived$ column is not TrueLists all executions of a procedure
bnch$procedure_method_execution_instance_assoc$beta
bnch$procedure_method_execution_instance$betaarchived$ column is not True
bnch$procedure_method_task_transition$beta
bnch$procedure_step_execution_instance$betaarchived$ column is not True
bnch$parameter_planned_value$betaThe expected value for a parameter for a particular procedure run
bnch$parameter_confirmation_value$betaThe confirmed value for a parameter for a particular procedure run, filled in by the operator
bnch$parameter_measured_value$betaThe measured value of a parameter during the course of executing a procedure
bnch$parameter_value_plate_well$beta
bnch$procedure_run_condition$beta
bnch$procedure_run_condition_replicate$betaA single replicate of a condition. The UI doesn't have a singular term for this.
bnch$procedure_method_condition_replicate$beta
bnch$library_parameter_definition$alphaLists all the parameter library definitions
bnch$procedure_run_plan$beta

Recipe Run Plans (for Process Development Studies) and Assay Run Plans (for Assay-based Studies) are both saved as Procedure run plans in the warehouse.

This is essentially a draft procedure run. It becomes a procedure run (Recipe Run or Assay Run) once promoted.

bnch$procedure_run_plan_condition$betaA single condition in a single Procedure run plan.
bnch$run_plan_parameter_planned_value$beta

A planned link from a to-be-created unit operation instance to an actual unit operation instance.

These planned links become rows in bnch$procedure_method_execution_instance_assoc$beta once a procedure run is promoted.

bnch$proc_run_plan_condition_replicate$betaA single replicate within a Procedure run plan condition.
bnch$proc_run_plan_cond_repl_src_mapping$beta

A planned link from a to-be-created unit operation instance to an actual unit operation instance.

These planned links become rows in bnch$procedure_method_execution_instance_assoc$beta once a procedure run is promoted.


bnch$procedure_run$beta

This object lives in a project and has method execution instances that are associated with Workflow tasks that the user will work through. Also referred to as an experiment run in the UI.

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpcr_oPQS40h3Primary key for a table
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
descriptionDescription of object in BenchlingCharacter Varying
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
study_idUnique identifier for the parent study of the procedure runForeign key for study.idstdy_iG0LW1XU
procedure_idUnique identifier for the template procedure that the procedure run was created fromCharacter Varyingpc_aX3ST2SH
archived$Archival state for object in BenchlingBooleanTRUE, FALSETrue indicates the object is archived
archive_purpose$Archival reason for object in BenchlingTextnull, Made in Error, Retired, Other, etcnull indicates the object is not archived

bnch$procedure_method_execution_instance_assoc$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpcmeiasn_gRzqEGdoPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
source_procedure_method_execution_instance_idUnique identifier for source procedure method execution instanceForeign key for procedure method executon instance .idpcmei_gLZqJzcl
target_procedure_method_execution_instance_idUnique identifier for target procedure method execution instanceForeign key for procedure method executon instance .idpcmei_zsGLtpSo

bnch$procedure_method_execution_instance$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpcmei_Bz5Dlmu5Primary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
procedure_run_idUnique identifier for parent procedure runCharacter Varyingpcr_gLZqJzcl
workflow_task_idUnique identifier for associated Workflow taskForeign key for workflow_task.idwftask_gLZqJzcl
worksheet_idUnique identifier for associated worksheetForeign key for worksheet.idwks_gLZqJzcl
archived$Archival state for object in BenchlingBooleanTRUE, FALSETrue indicates the object is archived
archive_purpose$Archival reason for object in BenchlingTextnull, Made in Error, Retired, Other, etcnull indicates the object is not archived

bnch$procedure_method_task_transition$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingent_yXrL3BjX, etr_GtcscEZq, loc_Y2v8daz0, etcPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
method_execution_instance_idUnique identifier for the associated method execution instanceForeign key for procedure_method_execution_instance.idpmei_hh9ffHqV
transitioned_atTime entered when the associated Workflow task was transitioned to the status specified in status_display_nameTimestamp without timezone2019-12-06T23:24:44.885478
status_display_nameStatus of Workflow task associated with the methodCharacter VaryingIn progress, Failed, Skipped
commentComment, if any, associated with transitioning (starting, completing, skipping, or failing) the methodCharacter VaryingDelayed

bnch$procedure_step_execution_instance$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpcsei_bwmh3o3sPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
positionZero-indexed position of the step within a step groupInteger0, 1
step_group_typeType of the parent step groupCharacter VaryingPRE_RUN, RUN
workflow_task_idUnique identifier for associated Workflow taskForeign key for workflow_task.idwftask_gLZqJzcl
archived$Archival state for object in BenchlingBooleanTRUE, FALSETrue indicates the object is archived
archive_purpose$Archival reason for object in BenchlingTextnull, Made in Error, Retired, Other, etcnull indicates the object is not archived

bnch$parameter_planned_value$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingppvdp_IBZ9BA8GPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
method_execution_instance_idUnique identifier for the associated method execution instanceForeign key for procedure_method_execution_instance.idpmei_hh9ffHqV
parameter_typeParameter type of the parent parameterCharacter VaryingEQUIPMENT, MATERIAL_INPUT, MATERIAL_OUTPUT, DATA_PARAMETER
parameter_idUnique identifier for the parent parameterCharacter Varyingpcparam_cCO8Dvfc
valueThe planned value for the parameterJSON value350, null, bfi_GuPYFZQH, water
typeData type of the parent parameter versionCharacter Varyingentity_link, text, float
unit_idUnique identifier for the unit associated with the parent parameter versionForeign key for unit.idnull, unit_aWP1Asqp
amountThe planned amount for a material input. Will always be null for other parameter types.Floating pointnull, 4.2
amount_unit_idUnique identifier for the amount unit for a material input. Will always be null for other parameter types.Foreign key for unit.idnull, unit_aWP1Asqp
container_idUnique identifier for the associated containerForeign key for container.idnull, con_wQM2Lshs

bnch$parameter_confirmation_value$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingppvdc_CKErwORTPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
method_execution_instance_idUnique identifier for the associated method execution instanceForeign key for procedure_method_execution_instance.idpmei_hh9ffHqV
parameter_typeParameter type of the parent parameterCharacter VaryingEQUIPMENT, MATERIAL_INPUT, MATERIAL_OUTPUT, DATA_PARAMETER
parameter_idUnique identifier for the parent parameterCharacter Varyingpcparam_cCO8Dvfc
valueThe planned value for the parameterJSON value350, null, bfi_GuPYFZQH, water
typeData type of the parent parameter versionCharacter Varyingentity_link, text, float
unit_idUnique identifier for the unit associated with the parent parameter versionForeign key for unit.idnull, unit_aWP1Asqp
amountThe planned amount for a material input. Will always be null for other parameter types.Floating pointnull, 4.2
amount_unit_idUnique identifier for the amount unit for a material input. Will always be null for other parameter types.Foreign key for unit.idnull, unit_aWP1Asqp
container_idUnique identifier for the associated containerForeign key for container.idnull, con_wQM2Lshs
recorded_atThe date/time that the parameter was confirmed, or for material inputs, was addedTimestamp without time zonenull, 2024-09-06T14:38:29
commentComment, if any, associated with the parameter confirmationCharacter VaryingUsing more saltBlank comments are stored as an empty string

bnch$parameter_measured_value$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingppvda_psx3VtGYPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
method_execution_instance_idUnique identifier for the associated method execution instanceForeign key for procedure_method_execution_instance.idpmei_hh9ffHqV
parameter_typeParameter type of the parent parameterCharacter VaryingEQUIPMENT, MATERIAL_INPUT, MATERIAL_OUTPUT, DATA_PARAMETER
parameter_idUnique identifier for the parent parameterCharacter Varyingpcparam_cCO8Dvfc
valueThe planned value for the parameterJSON value350, null, bfi_GuPYFZQH, water
typeData type of the parent parameter versionCharacter Varyingentity_link, text, float
unit_idUnique identifier for the unit associated with the parent parameter versionForeign key for unit.idnull, unit_aWP1Asqp
amountThe planned amount for a material input. Will always be null for other parameter types.Floating pointnull, 4.2
amount_unit_idUnique identifier for the amount unit for a material input. Will always be null for other parameter types.Foreign key for unit.idnull, unit_aWP1Asqp
container_idUnique identifier for the associated containerForeign key for container.idnull, con_wQM2Lshs
recorded_atThe date/time that the parameter was confirmed, or for material inputs, was addedTimestamp without time zonenull, 2024-09-06T14:38:29
commentComment, if any, associated with the parameter confirmationCharacter VaryingUsing more saltBlank comments are stored as an empty string

bnch$parameter_value_plate_well$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingent_yXrL3BjX, etr_GtcscEZq, loc_Y2v8daz0, etcPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
plate_idUnique identifier for the plateForeign key for plate.idplt_wQM2Lshs
parameter_confirmation_value_idUnique identifier a confirmed parameter valueForeign key for parameter_confirmation_value.idppvc_aWP1Asqp
parameter_planned_value_idUnique identifier a planned parameter valueForeign key for parameter_planned_value.idppvp_aWP1Asqp
well_positionPosition of the plate well where the parameter value was confirmedCharacter VaryingA3

bnch$procedure_run_condition$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpcrc_V8dmqCiMPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
nameName of object in BenchlingCharacter VaryingTransfection Entry, QC Results, Therapeutic Cell Line, etc
descriptionDescription of the conditionCharacter VaryingControl
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
procedure_run_idUnique identifier for the parent procedure runForeign key for procedure_run.idprc_wa2kjuQaQ

bnch$procedure_run_condition_replicate$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprcr_nuBvDwbnPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
condition_idUnique identifier for the parent conditionForeign key for procedure_run_condition.idpcrc_wa2kjuQaQ
replicate_numberUnique identifier for the replicate within the condition groupInteger1

bnch$procedure_method_condition_replicate$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingent_yXrL3BjX, etr_GtcscEZq, loc_Y2v8daz0, etcPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
procedure_run_condition_replicate_idUnique identifier for a specific replicate of a conditionForeign key for procedure_run_condition_replicate.idprcr_qHF3HNaT
method_execution_instance_idUnique identifier for the execution instance of a method (unit operation) for a replicate of a conditionForeign key for procedure_method_execution_instance.idpcmei_Bz5Dlmu5

bnch$library_parameter_definition$alpha

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingpardef_vV99UJsKLdPrimary key for a table
nameName of object in BenchlingCharacter VaryingTemperature
descriptionDescription of object in BenchlingCharacter Varying
typeData type of the parameterCharacter Varyingfloat, datetime, text
unit_type_idUnit type (mass, time, length, concentration etc)Foreign key for unit_type.idqnty_z8erUgSOcF

bnch$procedure_run_plan$beta

This is the draft version of a procedure run. Represents either a planned Recipe Run or Assay Run. Once a the plan is promoted, procedure_run_id references the resulting procedure_run row.

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprp_aX3ST2SHPrimary key for a table
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
study_idUnique identifier for the parent study of the procedure run planForeign key for study.idstdy_iG0LW1XU
descriptionDescription of the procedure run plan.Character VaryingBecomes the description of the procedure run on promotion.
data_entry_modeHow data is entered across condition replicates during a procedure runCharacter VaryingINDIVIDUAL_CONDITION_REPLICATES, ALL_CONDITION_REPLICATES_TOGETHERINDIVIDUAL_CONDITION_REPLICATES creates one worksheet per condition-replicate; ALL_CONDITION_REPLICATES_TOGETHER creates a single shared worksheet.
process_flowchart_config_version_idThe ID of the specific version of the Recipe or Assay that will be used for this planned run (or was used in the case of a promoted run plan)Character Varyingwffccv_gLZqJzcl
procedure_run_idUnique identifier for the procedure run started from this planForeign key for procedure_run.idnull, pcr_gLZqJzclnull until a procedure run has been started from the plan.
confirmation_method_by_param_version_idMapping from parameter version id to the confirmation method that should be used for that parameter during executionJSONB{"schver_abc123": "TABLE", "schver_def456": "PLATE_MAP"}Values are TABLE (entered via a structured notebook table) or PLATE_MAP (entered via a plate-map layout, one value per well).

bnch$procedure_run_plan_condition$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprpc_V8dmqCiMPrimary key for a table
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
nameName of the conditionCharacter VaryingControl, High pH, C1, V100
procedure_run_plan_idUnique identifier for the parent procedure run planForeign key for bnch$procedure_run_plan$beta.idprp_wa2kjuQaQ
template_method_version_idUnique identifier for the template procedure method definition version this value is planned againstCharacter Varyingpcmdv_gLZqJzcl
descriptionDescription of the conditionCharacter VaryingTesting high pH during culture

bnch$run_plan_parameter_planned_value$beta

Planned Parameters, Materials, and Equipment values are all stored in this “Parameters” table. The parameter_type column tells you which is which.

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprpc_V8dmqCiM_0_pcmdv_ABC123_schver_XYZ789_0Primary key for a table. Composite key composed of the condition id, template method version id, parameter version id, and a zero-indexed value index.
creator_idUnique identifier for creator of objectForeign key for user.ident_yXrL3BjX
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
created_atCreated date for objectTimestamp without timezone2024-08-20T14:53:15.458544
modified_atMost recent modified date for objectTimestamp without timezone2024-08-23T13:34:03.96262
procedure_run_plan_idUnique identifier for the parent procedure run planForeign key for bnch$procedure_run_plan$beta.idprp_wa2kjuQaQ
procedure_run_plan_condition_idUnique identifier for the parent procedure run plan conditionForeign key for bnch$procedure_run_plan_condition$beta.idprpc_wa2kjuQaQ
parameter_version_idUnique identifier for the parameter version this value is planned againstCharacter Varyingschver_gLZqJzcl
value_indexZero-indexed position of this planned value within the parameter's planned valuesInteger0, 1Supports parameters that have more than one planned value.
nameName of the parameterCharacter VaryingTemperature, Buffer, Plate ReaderFor library-backed parameters, sourced from the library; otherwise sourced from the recipe.
parameter_typeParameter type of the parameterCharacter VaryingEQUIPMENT, MATERIAL_INPUT, MATERIAL_OUTPUT, DATA_PARAMETERParameters, Materials, and Equipment are all stored in this “Parameters” table. This column tells you which is which.
typeData type of the parent parameter versionCharacter Varyingentity_link, text, float
parameter_idUnique identifier for the parent parameterCharacter Varyingpcparam_cCO8Dvfc
parameter_library_idUnique identifier for the backing library parameter definition, if the parameter is library-backedForeign key for library_parameter_definition.idnull, pardef_vV99UJsKLdnull when the parameter is not library-backed.
valueThe planned value for the parameterJSON value350, null, bfi_GuPYFZQH, water
unit_idUnique identifier for the unit associated with the parent parameter versionForeign key for unit.idnull, unit_aWP1Asqp
amountThe planned amount for a material input. Will always be null for other parameter types.Floating pointnull, 4.2
amount_unit_idUnique identifier for the amount unit for a material input. Will always be null for other parameter types.Foreign key for unit.idnull, unit_aWP1Asqp

bnch$proc_run_plan_condition_replicate$beta

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprpc_V8dmqCiM_1Primary key for a table. Composite key composed of the parent condition id and the replicate number.
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
procedure_run_plan_condition_idUnique identifier for the parent procedure run plan conditionForeign key for bnch$procedure_run_plan_condition$beta.idprpc_wa2kjuQaQ
replicate_numberUnique identifier for the replicate within the conditionInteger1, 2

bnch$proc_run_plan_cond_repl_src_mapping$beta

Maps to-be-created Unit Operation instances to actual Unit Operation instances in the Study. These planned links become rows in bnch$procedure_method_execution_instance_assoc$beta once a procedure run is promoted.

Table RowDefinitionValue TypeExample values (if applicable)Notes
idUnique Benchling-prescribed ID for each line item in tableCharacter Varyingprpc_V8dmqCiM_1_pcmdv_ABC123_pcmei_XYZ789Primary key for a table. Composite key composed of the replicate id, template procedure method definition version id, and source procedure method execution instance id.
source_idThe id of the project that the object's permissions comes fromForeign key for project.idsrc_hh9ffHqV
procedure_run_plan_condition_replicate_idUnique identifier for the parent planned condition replicateForeign key for bnch$proc_run_plan_condition_replicate$beta.idprpc_V8dmqCiM_1
template_pmdv_idUnique identifier for the template procedure method definition version being planned for this replicateCharacter Varyingpcmdv_gLZqJzcl
source_method_execution_instance_idUnique identifier for the upstream source procedure method execution instance that will feed this replicate once a procedure run is promoted.Character Varyingpcmei_gLZqJzcl


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