Notebook

Benchling Notebook acts as an ELN for users to log their experiments, create protocols, and capture results against their samples.


Box Creation Tables in Notebook Entries

Users can now use Box Creation tables in Notebook entries to generate new boxes for entity storage in Inventory. Similar to how Registration tables function, users will be able to use Box Creation tables to easily track and create boxes within a Notebook entry. This feature makes it more intuitive to create boxes and mirrors actual use cases in the lab where large number of samples are created from an experiment and stored in boxes right after.

Molecular Biology

Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.

Configuration for Bulk Back Translation

In the past, Back Translation could only be performed on one amino acid entity at a time. With this update, you can select multiple amino acid entities and Back Translate in bulk. This features increases throughput and reduces tedious, repetitive steps in sequence analysis. Currently, a configuration flag needs to be flipped to allow for bulk Back Translation in a tenant. When enabled, the user can select multiple AA entities in the expanded view of the registry, navigate to ‘More’, select ‘Analyze’, and then select ‘Back Translate’. Please contact support@benchling.com to enable.


Registry and Inventory

The Registry and Inventory combine to form an extremely powerful solution for life sciences R&D samples. The Registry can be used to model and log any biological entities while the Inventory provides an interactive digital window into the physical storage system of your lab.

Bioentity Alias is Now Stored in the Warehouse

Until this point, Bioentity alias’ (alias’ of DNA and AA sequence entities, for example) were not stored in the Warehouse. This eliminated Alias’ from use in Insights. The alias’ of Bioentities are now stored in the Warehouse table column ‘entity'_alias', allowing for queries to be performed using these identifiers.

Batches Eliminated from Transfer Modal and Registration Tables

When batches are disabled on a tenant, the batch option in transfer modals and registration tables will no longer be accessible. This will ensure that batches are entirely disabled on tenants where batches are not configured and thus avoid confusion for users.

Adjustments in Cut Line for Printer to Cut Multiple Label Sets

When printing multiple rows of the same label (a label set), we can program printers to automatically cut the label sheet after the labels are printed. This setting is configurable to adjust to the number of labels you will have per row, where in row 18, the value for C should be set to the number of labels per row (for example, to set 4 labels per table row, C should have a value of 4)

m i
zO
J circlelbl
j 3167963641665406
S l1;0,0,0.63,0.75,1.85;circlelbl
H 3.937,0,T,R0,B0
O R,P
B:Barcode2;1.5336,0.0808,0,datamatrix,0.0115;benchling.entity.name
T:Text01;0.0149,0.0952,0,5,0.1087,b,k;benchling.entity.Plasmid
T:Text02;0.017,0.2087,0,3,0.1083,k;benchling.entity.name
T:Text03;0.0149,0.3241,0,5,0.1,b,k;benchling.entity.Prep Date
T:Text05;0.0139,0.4458,0,3,0.1,k;benchling.entity.Final Concentration (mg/mL)
T:Text07;0.0149,0.5762,0,5,0.0799,b,k,q99;benchling.entity.creator
T:Text04;0.7068,0.3225,0,5,0.1008,b,k;benchling.entity.Project
T:Text06;0.7068,0.4448,0,3,0.1,k;(mg/mL)
G0.6588,0.2561,270;L:0.0679,0.0012,s,s
T:Text08;1.373,0.2933,0,3,0.06,k;[J:c0.477]benchling.entity.Plasmid>>registry_id
C 1
A 1




Create child entities on unregistered parent entities

Previously, the (+) icon to create child entities was only available when the parent was registered, leading to inflexible creation of cancer cell lots or plasmid preparations when their associated parents were not registered. This gives the researcher the ability to create child entities during experiments on the fly without worrying about the parent.


Bulk update registry IDs via spreadsheet

A new adapter column was added for changing registry IDs in bulk. In the past, changes to multiple registry IDs required assistance from Benchling support. Now users can easily update registry IDs in bulk through the update entities feature in the registry.

Bulk import locations via spreadsheet

Previously, locations could be bulk imported to Benchling only with a request to Benchling Support. With this feature addition, users are equipped to import multiple locations into Benchling directly from the Storage tab using a spreadsheet.


Bulk update boxes via spreadsheet

Boxes can now be updated in bulk using a spreadsheet. This feature can be accessed by navigating to storage, selecting ‘Create’, selecting ‘Boxes’, and finally ‘Update Boxes’. In the past, users required the help of Benchling support to accomplish bulk updates to boxes and therefore this feature further promotes user autonomy and productivity.

Bulk update plates via spreadsheet

Plates can now be updated in bulk using a spreadsheet. Users can utilize this feature by navigating to storage, selecting ‘Create’, ‘Plates’, and finally ‘Update Plates’. Updating plates in bulk previously required the help of Benchling support. As this is no longer needed, this update boosts user productivity and saves time.

Changes to container contents reflect in the container audit log

The exported audit log (red, underlined icon) exports history relevant to a particular container as a CSV. Now, changes to the container contents are also recorded in the audit log, increasing traceability of container contents over time.

Example of an audit log: {"item": "AVial049", "containerContents": {"updated": [{"current": {"item": "melanoma_cell_1", "concentration": {"units": "cells/uL", "value": 10000.0}, "type": "custom_entity", "id": "bfi_zNm6aXIL"}, "previous": {"item": "melanoma_cell_1", "concentration": {"units": null, "value": null}, "type": "custom_entity", "id": "bfi_zNm6aXIL"}}], "removed": [], "added": []}, "barcode": "AVial049", "type": "container", "id": "con_xXP3BLPM"}


Schemas

Set the Precision of Float Fields in Result Schemas

Float fields in Result schemas are now configurable to a desired precision level. The user can use the string ‘decimalPrecision’ followed by an integer to specify the precision desired (ex. “decimalPrecision”: 3 would record results to the thousandths position, 0.000).

Insights

Insights is one of our newest applications to the platform. This feature is seamlessly integrated with all Benchling applications, and enables users to query, visualize, and share high quality, structured data that resides on the platform.

Dynamic Warehouse Diagrams via Schema Browser

We have added a new interactive way to query from the Warehouse in the Insights Dashboard. Dynamic Warehouse Diagrams enhance the user experience by enabling users to visually interact with the Warehouse. To access the Diagrams, select an entity in the Schema Browser, then select the ‘open entity diagram’ icon in the top right.


Request Chips in Requests Dashboards

There are now interactive chips for Requests in the Requests Dashboard. The chip text is the Request Name and when selected from Requests Dashboard it will open a tab in the workspace with details on the Request. Until now, there was no interactive modality in the Request Dashboard for accessing information about queried Requests.


Lab Automation

Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.

Use Run Schema Field to Auto-fill Entity Fields Being Created

In Lab Automation, you can now hoist information from run schema fields in order to populate fields in entities generated through a Lab Automation run. The specification of which schema field the user is looking up enables Lab Automation to auto-fill fields in the entity.

Use Request Task Schemas in Multiple Request Templates

In the past, Request task schemas were only useable in one Request template. With this update, Request task schemas can be used in more than one request template.

App Platform

Added Option to Filter by Empty DNA Sequences

It is now possible to filter queries to include DNA sequence entities that have empty DNA sequences. This will allow for quick searches of DNA sequence entities that do not have a DNA string inputted yet. Navigate to ‘Filter’, select ‘Add Filter’, select ‘DNA String’ from the dropdown on the left, and then select 'is empty’ from the right dropdown.

Dev Platform

Our developer platform is fundamental to centralizing and standardizing all your R&D data. Benchling’s APIs are built to match the flexibility and speed of modern life science R&D.

Added Option to Filter by Unregistered Entities

There is a new option to filter by unregistered entities when querying through the Benchling API. Previously, there was no way to parse between registered and unregistered entities within the developer platform. Now, you can specify ‘null’ in the ‘RegistryId’ string to filter for only unregistered entities.(https://docs.benchling.com/reference#list-dna-sequences)

Bug Fixes

The following bugs were fixed in this release:

Notebook:

  • Fixed limited display of history tab when there is a long entry history and the zoom is set to < 100%.
  • Performance of the ‘Results Tab’ for entities with greater than 50 results has been improved to load faster.
  • The following actions are now prevented on read-only Entries: delete tables by selecting all rows, replace excerpts, check out files, and clicking table toolbar buttons. Previously these actions would lead to a crash.

Example: Read-only table with table toolbar greyed out

  • Replacing an excerpt actually replaces instead of inserting - previously, the “replace excerpt”leaf icon would lead to insertion.
  • Registration tables can now be submitted, even with archived items within the table. Before, the table would have resulted in an error, and unarchived entities were not able to be updated as soon as the table encountered this error. Now, there will be a warning, but the registration will go through for unarchived entities, leaving the archived ones untouched.

Molecular Biology

  • Increased reliability for importing MacVector sequence files
  • Creating a DNA sequence from selection should copy over description properly when selected.

App Platform

  • Fixed failure to bulk update by entity name.
  • Don’t allow users to invite themselves to an org they create - previously, the creator of an organization was able to add themselves as a member to an organization, although they were already populated.
  • Fixed the error message that a user gets if they type invalid data into the user creation tool - an error in the email field will lead to “not an email” error, as opposed to the previous error:“user information cannot be empty”.

Developer Platform

  • Fixed the error object so it properly returns on bulk entity endpoint.
  • Lab Automation APIs now properly create results tables. Previously, the output table of results was not consistently displayed, even when the result file was successfully patched and processed.

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