A computed field is a specialized field type for entities, which is automatically computed and recomputed based on other values in the system. In this way, you can for example display a field from a parent entity onto the child entity, calculate the MW of your protein entities or calculate the average of all results recorded against this entity.

Computed field values can be pulled or calculated directly from a field on the entity OR pulled from other entities that are directly linked to the entity through (a chain of) entity links. Results can also be pulled onto an entity when they are directly associated with the entity.

What do computed fields look like in Benchling?

Computed fields are automatically denoted with the fx symbol, and can be observed directly on the schema, along with any other regular schema field types.

The contents of these fields will be calculated automatically based on other data related to this entity, and can thus not be modified by hand. Computed fields are always up-to-date as they are recalculated automatically when the values they are based on are updated.

Examples of computed fields

To understand how these fields could integrate with data within Benchling please see visual below as well as a few examples by computed field type.

Showing all Primers on the DNA sequence

Days between dates

Aggregate Entity Links

How do I configure a computed field in Benchling?

At the moment, computed fields can only be configured by Benchling Support. Registry admins can request a computed field through the in-app support chat or support@benchling.com. Please provide the following information when requesting a computed field:

  • The schema on which the computed field should be added.

  • The name of the new computed field. Note that the name of the computed field must be unique.

  • The type of computed field.

  • The lineage of information, if data is to be pulled from other schemas through existing entity links. If you can provide a diagram, that would work best.

Computed fields cannot be modified, only created anew. However, if modification is needed, we can archive the existing computed field and create a new one from scratch.

What computed field types are supported in Benchling?

The tables below list all computed fields that can be configured in Benchling, and brief of description of what each field type hoists or calculates. These computed fields can be split in different categories based on their usage.

Molecular Biology & Chemistry

These computed fields help you to easily calculate properties of DNA and AA sequences, or render the chemical structure.

Computed Field Type

Field Definition

DNA parent

What sequence this sequence is derived from (through clone/copy)

DNA sequence CpG

Compute the count of CG bases appearing together in a DNA sequence

DNA sequence GC%

Surface the GC% of a DNA sequence

DNA sequence Tm

Surface the Tm (Melting Temperature) of a DNA sequence using SantaLucia parameters

DNA to RNA

Translate a DNA sequence to RNA by replacing the Ts with Us. This does not return the reverse complement.

Get primers of schema

Show all attached primers on given DNA entity

RNA extinction coefficient

Calculate the extinction coefficient for an RNA sequence. This formula can also be used on DNA sequences, where it will assume Ts are Us.

RNA sequence Tm

Surface the Tm (Melting Temperature) of an RNA sequence using Xia parameters

Protein Instability Index

Calculate the instability index of a AA entity sequence and indicate if it's stable or unstable.

Protein complex absorbance (Cys-oxidized)

Calculate the absorbance assuming all Cys AAs have formed disulfide bonds

Protein complex absorbance (Cys-reduced)

Calculate the absorbance assuming no Cys AAs have formed disulfide bonds

Protein complex extinction coefficient (Cys-oxidized)

Calculate the extinction coefficient across multiple linked AA entities assuming all Cys AAs have formed disulfide bonds

Protein complex extinction coefficient (Cys-reduced)

Calculate the extinction coefficient across multiple linked AA entities assuming no Cys AAs have formed disulfide bonds

Protein complex MW (Da) (Cys-oxidized)

Calculate the MW across multiple linked AA entities. Defined as sum(weights of individual amino acids) - 1 water per amide bond - 2 hydrogen per possible disulfide bond

Protein complex MW (Da) (Cys-reduced)

Calculate the MW across multiple linked AA entities. Defined as sum(weights of individual amino acids) - 1 water per amide bond

Protein complex pI

Calculate the pI across multiple linked AA entities

Single chain MW (Da)

Calculate the MW of a single AA entity (Da)

Single chain MW (kDa)

Calculate the MW of a single AA entity (kDa)

Chemical Structure from SMILES

Render the chemical structure from a SMILES string in a text field on the entity

Aggregating and Hoisting values

These computed fields help you to directly display values from linked entities or aggregate values. When aggregating values, you can choose to have all values unsorted with duplicates, or deduplicated and sorted.

Computed Field Type

Field Definition

Aggregate Dropdowns

Hoist Dropdown values

Aggregate Entity links

Hoist Entity Links

Aggregate Entry links

Hoist Entry Links

Aggregate Text values

Hoist Text value

Hoist Date

Hoist Date fields

Hoist Floating Point

Hoist Floating Point fields

Hoist Integer

Hoist Integer fields

General calculations

These computed fields can do simple calculations with entity field values.

Computed Field Type

Field Definition

Sum

Calculate the sum of up to 4 integers or floats.

Subtract

Subtract one value from another. Can take entity fields, constant values, results fields, etc.

Multiply with exponents

(x1 ^ e1) * (x2 ^ e2) * ... etc

Multiply (with exponents if needed) up to 5 values on an entity. The values don't have to be a field value on the entity; they can be a constant floating point value as well.

Subtract dates/datetimes

Calculate the difference between Date or Datetime fields in days, hours, minutes or seconds.

Number of links

Calculate the number of linked entities in a specific field

First text value that is non-empty

Shows the first non-empty value from a prioritized list of up to 10 fields

Concatenate Text

Link text together in a chain or series

Text length

Evaluate the length of the string e.g. "ABC" = 3. This can also be used to calculate the DNA base pair length.

Filter to registered entities

Filter the values from an entity link field to only display unregistered entities

Filter to registered entities

Filter the values from an entity link field to only display registered entities

Nth entity of list

Select the Nth (where N is an integer) entity link from a multi-select entity link field

Resurfacing results to the entity

These computed fields allow you to pull a specific field from a result table associated to the entity into the schema fields.

Computed Field Type

Field Definition

Hoist field from most recently created result

Surface field from most recent data recorded in a specific result table associated with that entity

Mean of field from results

Calculate the average of a field within a specific result table associated with that entity

Standard Deviation of field from results

Calculate the STD of a field within a specific result table associated with that entity

Sum of field from results

Sum all of the values of a field within a specific result table associated with that entity

Max of field from results

Surface the maximal field value within a specific result table associated with that entity

Min of field from results

Surface the minimal field value within a specific result table associated with that entity

At the moment, custom formulas are not supported. However, if you have any ideas for computed field formulas that would be useful to your team, feel free to submit them for consideration through our in-app support chat or at support@benchling.com.

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