Computed fields automatically calculate a value based on other values in your Benchling tenant. For an overview of what computed fields are and how they work, visit Computed fields basics.
Snapshot fields
Users can configure snapshot fields, a type of computed field, on results and workflows schemas to look up data from anything that is linked to inventory or registry items. Unlike other computed fields however, snapshot fields are frozen in time.
For workflows schemas computed, snapshot fields are calculated twice, this is done to surface the most current data for users when executing tasks:
- When the task is created
- When the task is executed
Configuring Benchling to capture results at a specific point in time enables you to view and query this information in context with experiments, workflows, and the sample itself. Snapshot fields can be used many ways, some of which include:
-
The ability to record results against a sample’s container
-
Teams can associate results with wells and containers in their inventory.
-
-
Automatic data entry
-
Scientists can automatically populate a results table with a sample’s metadata.
-
Field types and definitions
The tables below list configurable computed fields and a brief description of what each field type pulls (hoists) or calculates. They are organized based on what they’re used for:
Molecular Biology
These computed fields help calculate properties of DNA and AA sequences.
| Field type | Field definition |
|---|---|
| DNA parent | Which sequence this sequence is derived from (through clone or 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 Ts with Us. This does not return the reverse complement |
| Get primers of schema | Display attached primers on a 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 of an RNA sequence using Xia parameters |
| Protein Instability Index | Calculate the instability index of an 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 (molecular weight) 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) |
| Single-stranded DNA MW | Calculate the MW of a single-stranded DNA entity (Da) |
Chemistry
These computed fields calculate properties of molecules and chemical compounds, or render the chemical structure.
| Field type | Field definition |
|---|---|
| Aromatic ring count | Return the number of aromatic rings in the molecule |
| Atom count | Return the number of atoms in the molecule |
| Chemical Structure from SMILES | Render the chemical structure from a SMILES string in a text field on the entity |
| Exact molecular weight | Calculate the MW based on only the most abundant isotopes of each atom |
| Heavy atom count | Return the total number of non-hydrogen atoms within the chemical structure |
| Hydrogen acceptor count | Calculate the number of groups that can accept the hydrogen atom of a hydrogen bond; typically O or N |
| Hydrogen donor count | Calculate the number of groups that supply the hydrogen atom of a hydrogen bond; typically O-H or N-H bonds |
| LogP | Calculate the partition coefficient of a molecule between lipophilic and aqueous phases usually considered as octanol and water. Values > 1 indicate a preference for the lipophilic phase |
| Molar refractivity | Calculate the total polarizability of a mole of a substance; dependent on the temperature, the index of refraction, and the pressure. Most drugs have a value between 40-130 |
| Molecular weight (Molecule) | Calculate the MW based on the weighted averages of all isotopes of each atom present |
| Ring count | Return the number of rings regardless of aromaticity |
| Rotatable bond count | Return the number of rotatable bonds, defined as any single bond, not in a ring, bound to a nonterminal heavy atom. Excluded from the count are amide C–N bonds because of their high rotational energy barrier |
| sp3 atom count | Return the number of sp3 atoms (think tetrahedral geometry, like Methane). For C, O, and N, this means only single bonds |
| TPSA | Return the topological polar surface area (TPSA) of a molecule, defined as the surface sum over all polar atoms or molecules, primarily oxygen and nitrogen, also including their attached hydrogen atoms. Does not account for 3D structure and is often used as a rough indicator of a compound's ability to be absorbed inside a body. Higher values indicate higher polarity |
Aggregating and hoisting values
The computed fields in the table below help display values from linked entities or aggregate values. When aggregating values, you can choose to have values unsorted with duplicates, or sorted and deduplicated.
| 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
The computed fields in the table below do calculations with entity field values.
| Field type | Field definition |
|---|---|
| Concatenate Text | Link text together in a chain or series |
| Filter to registered entities | Filter the values from an entity link field to only display registered entities |
| Filter to unregistered entities | Filter the values from an entity link field to only display unregistered entities |
| First text value that is non-empty | Shows the first non-empty value from a prioritized list of up to 10 fields |
| Log | Compute the logarithmic value of a specified field, and specify appropriate log base |
| 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 |
| Nth entity of list | Select the Nth (where N is an integer) entity link from a multi-select entity link field |
| Number of links | Calculate the number of linked entities in a specific field |
| Subtract | Subtract one value from another. It can take entity fields, constant values, results fields, etc. |
| Subtract dates/datetimes | Calculate the difference between Date or Datetime fields in days, hours, minutes or seconds |
| Sum | Calculate the sum of up to 4 integers or floats |
| Text length | Evaluate the length of the string e.g. "ABC" = 3. This can also be used to calculate the DNA base pair length |
Resurface results to the entity
Use the computed fields in the table below to pull a specific field from a results table associated with 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 |
| 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 |
| 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 |
Custom formulas
At this time, custom formulas are not supported. However, if you have feedback or ideas for computed field formulas that would be useful to your team, you can submit them for consideration through our in-app support chat or support@benchling.com.