Welcome to the third volume of our 2023 product release notes! We’ve been working hard to bring you performance improvements that add value to your work. Read on to learn about the product enhancements and bug fixes released in March and April 2023.
Molecular Biology
Benchling’s Molecular Biology is a cutting edge in silico design tool that supports the latest scientific workflows.
Sequence version names are no longer editable [2023.3.MB.1]
Users cannot edit the name of sequence versions for molecular biology entities.
Small Molecule
The molecule entity in Registry helps users model and interact with chemical compounds throughout the platform, enabling users to draw, visualize, store, and search chemical structures.
Promoted HELM-based oligo API endpoints [2023.3.SM.1]
Users can now access the oligo endpoints that handle HELM if their tenant has modified nucleotides enabled.
Added monomer mapping option to natural base bulk oligo imports [2023.3.SM.2]
Users can now use monomer mapping when importing oligos via .csv and registering them via a Registration table. Monomer mapping gives users the option to provide natural bases and specify different modified monomers for each base. For example, pseudouracil replaces uracil.
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.
Entity transfer requirements
When transferring an entity from one container to another via any pathway in Benchling, like Lab Automation runs, spreadsheet imports, Inventory tables, or API, the transfer now requires:
- That the quantity be less than or equal to the source quantity [2023.3.RI.1]
- The contents be specified [2023.3.RI.2]
If the transfer quantity is greater than the source quantity, or the transfer contents aren’t specified, the transfer will automatically fail.
Add item position to label printing templates [2023.3.RI.3]
Users can now use the new label template keywords "position" and "coordinates" to display only the numeric position or coordinates of a container within a box or plate without the full location path.
Export audit logs for label templates [2023.3.RI.4]
Users can export audit logs for label templates by accessing label template configurations in Registry Settings.
Workflows
Workflows are a sequence of processes that are performed to answer a research question or synthesize new material. For example, synthesizing a new set of proteins from supernatants, or improving the transduction process.
Execution entry for tasks included in relevant items for task groups [2023.3.WF.1]
Users can now find execution entries for tasks in the Relevant Items tab for task groups.
For example, if the task group is flowchart-executed and the flowchart has node-level task groups with entry execution, relevant items will include entries that the node-level tasks were executed in.
UX improvement to configuring flowcharts [2023.3.WF.2]
Users can now save their progress on a template flowchart in the schema configuration and move to other configuration panels, like Adding Tasks or Adding Transitions, even if the flowchart is invalid. Note that the Task schema on an invalid flowchart template can be saved but not submitted.
Updates to flowchart creation window
Users can now:
- Create and propagate tasks about 10 times faster [2023.3.WF.3]
- More easily draw edges between nodes on a flowchart by drawing from a much larger area and dropping to anywhere on a node [2023.3.WF.4]
- View more contents of a flowchart during creation because the window size was increased [2023.3.WF.5]
Lab Automation
Benchling for Lab Automation enables seamless integration of Benchling to liquid handlers, plate readers, imaging instruments, and more.
Improved Runs inbox search [2023.3.LA.1]
Users can now apply filters in the Runs inbox for more precise searching. With this update, the free-text search box is no longer available, which searched schema fields and creator and created at data, but users can still search this data and narrow down their results with filters.
To enable this feature, contact a Benchling representative.
Transfer of multiple entities in output file processing [2023.3.LA.2]
Users can now transfer multiple Registry items into output containers when processing output files. Sample concentration is recalculated based on the container’s final volume.
Use runs to convert files containing a Custom Transform to a supported file type [2023.3.LA.3]
Users can now upload any file type to a run containing a Custom Transform where the output of that step is a tabular file. Previously, users could only upload tabular file forms natively supported by Lab Auto, like .csv, or .xlsx. Allowing Custom Transforms to handle both file type conversion and data reformatting extends the capability of performing Lab Auto integrations.
Compliance Controls
With Compliance Controls, gathering required information for compliance is simple, intuitive, and performant. The team’s primary focus is on our auditing platform but we also own exporting and archiving.
Point-in-time naming [2023.3.CC.1]
Users can now view the name of an object in audit logs as it was at a certain point in time. When the name of an object changes in the system, audited changes from the time of the change will display the new name of the object, while audited changes before the name change will continue to reference the old name.
Printer audit logs [2023.3.CC.2]
Users can now export audit logs for printer configurations and print request events for barcodes.
Studies
Manage in vivo studies with modern software designed for data capture, collaboration, and insights.
Calculate and display P-value for randomization [2023.3.ST.1]
Users can now view a one-way ANOVA-calculated P-value in the randomization UI.
Randomize by date of birth [2023.3.ST.2]
Users can now select a date of birth (DoB) as an attribute during the randomization process.
Block randomization for one metric [2023.3.ST.3]
When randomizing with only one metric, users can select the block randomization method instead of clustering.
Updates to Randomization Report and Export [2023.3.ST.4]
Users can now view the following in the Randomization Report and Export:
- Date of birth
- P-value for each metric
- Randomization method
Dosing Report export [2023.3.ST.5]
Users can now export a comprehensive list of all treatment doses administered in a given study by exporting the Dosing Report, a new report type, from the Export list.
Bug Fixes
The following bugs were fixed in March and April:
Notebook
- Benchling no longer adds an inaccurate number of events when bulk archiving and unarchiving results.
- .pdf attachments in Results tables now export correctly.
- Users can now select an auditor when switching back to legacy review process from new entry review processes.
Molecular Biology
- Modifications to a registered sequence’s metadata are now recognized in Benchling, allowing the “modified at” filter to work as expected.
- RNA matching now works correctly when creating primers and auto-annotating a sequence.
- Benchling now allows users to reindex sequences in the middle of a part when overlapping parts is enabled.
- Autofilling parts and translations is no longer unreasonably slow when there are multiple empty registered parts and AA sequences.
- Added missing audit events corresponding to sequence updates.
- Alignments were erroring when sequences were imported from the user’s computer.
- Updated blank error message and added descriptive text when importing AA sequences that have too long feature names.
Registry and Inventory
- Users can now scroll through the concentration units on Inventory tables.
- Can now include populate aliases key and successfully use /custom-entities:bulk-create endpoint.
- Entity modified at values not matching between API and audit logs.
- Archive rows called without row UUIDs in audits
Workflows
- Added Audit export button on Workflows structured tables.
- Can now “undo execution of task from row” in the Tasks table of the execution entry for unarchived tasks, even when the Tasks table contains archived tasks.
- Can now submit an execution entry for review even if a task in the Tasks table is archived
- When two users try to add a Request task to the same Request at the same time, the page crashed for the second user. It now raises an error instead.
- In the Schema Config UI, if the user makes changes that cause errors in the Template Flowchart, those errors are now cleared when clicking Cancel.