Resources

AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations.

Create and manage Benchling apps on your tenant

Results represent the output of assays that have been performed. You can customize the schemas of results to fit your needs. Results can link to runs, entities, and other types.

To learn more about creating results, click here.

Runs capture the details / parameters of a run that was performed. Results are usually nested under a run.

Export audit log data for Benchling objects.

Endpoints to help authenticate with the rest of the API resources.

Blobs are opaque files that can be linked to other items in Benchling, like assay runs or results. For example, you can upload a blob, then upload an assay result that links to that blob by ID. The blob will then appear as part of the assay result in the Benchling web UI.

Boxes are a structured inventory type, consisting of a grid of positions that can each hold one container. Unlike locations, there are a maximum number of containers that a box can hold (one per position).

Boxes are all associated with schemas, which define the type of the box (e.g. "10x10 Cryo Box") along with the fields that are tracked and the dimensions of the box.

Like all inventory, every Box has a barcode that is unique across the registry.

Benchling curates codon usage data for a variety of organisms to support operations such as Codon Optimization and Back Translation.

Containers are the backbone of sample management in Benchling. They represent physical containers, such as tubes or wells, that hold quantities of biological samples (represented by the entities inside the container). The container itself tracks its total volume, and the concentration of every entity inside of it.

Containers are all associated with schemas, which define the type of the container (e.g. "Tube") along with the fields that are tracked.

Like all inventory, every container has a barcode that is unique across the registry.

Benchling supports custom entities for biological entities that are neither sequences or proteins. Custom entities must have an entity schema set and can have both schema fields and custom fields.

Benchling allows users to configure their own fully-custom string representation formats for import/export of nucleotide sequences (including chemical modifications).

Data frames in Benchling represent tabular data that is not schematized. They contain columns with defined types and rows of data. Data frames are primarily used within specific Benchling applications. For example, in Benchling Analysis, each table is represented as a dataframe that is visible only within the analysis.

Similar to Data frames, datasets in Benchling represent tabular data that is not schematized. Datasets are saved to folders within Benchling with additional metadata, making them accessible and searchable within Benchling. Each dataset actually contains a data frame, and a data frame is required to create a dataset.

A DNA alignment is a Benchling object representing an alignment of multiple DNA sequences. This endpoint is deprecated, please migrate to the existing Nucleotide Alignments endpoints.

DNA Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.

DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.

Dropdowns are registry-wide enums. Use dropdowns to standardize on spelling and naming conventions, especially for important metadata like resistance markers.

Entities include DNA and AA sequences, oligos, molecules, custom entities, and other biological objects in Benchling. Entities support schemas, tags, and aliases, and can be registered.

Entries are rich text documents that allow you to capture all of your experimental data in one place.

Restriction enzymes are curated by Benchling for operations such as Digests and Codon Optimization.

The Events system allows external services to subscribe to events that are triggered in Benchling (e.g. plasmid registration, request submission, etc).

Export a Notebook Entry or a Legacy Workflow Stage Entry.

Feature Libraries are collections of shared canonical patterns that can be used to generate annotations on matching regions of DNA Sequences or AA Sequences.

Files are Benchling objects that represent files and their metadata. Compared to Blobs, which are used by most Benchling products for attachments, Files are primarily used in the Analysis and Connect product.

Folders are nested within projects to provide additional organization.

Instrument Queries are used to query the instrument service.

Manage inventory wide objects.

Lab Automation endpoints support integration with lab instruments, and liquid handlers to create samples or results, and capture transfers between containers at scale.

List label templates.

Legacy Workflows allow orchestrating complex experiments.

Please use endpoints for Legacy Workflows. These deprecated endpoints will be removed once users are migrated onto Legacy Workflows endpoints.

Manage locations objects.

Like all inventory, every Location has a barcode that is unique across the registry.

Mixtures are solutions comprised of multiple ingredients where the exact quantities of each ingredient are important to track. Each ingredient is uniquely identified by its component entity.

Molecules are groups of atoms held together by bonds, representing entities smaller than DNA Sequences and AA Sequences. Just like other entities, they support schemas, tags, and aliases.

Monomers are chemical building blocks with specified structures used to compose modified nucleotides. Note that monomer write endpoints require tenant admin permissions.

A Nucleotide Alignment is a Benchling object representing an alignment of multiple DNA and/or RNA sequences.

Oligos are short linear DNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.

Please migrate to the corresponding DNA Oligos endpoints so that we can support RNA Oligos.

View organization objects.

Plates are a structured inventory type, grids of wells that each function like containers. Plates come in two types: a traditional "fixed" type, where the wells cannot move, and a "matrix" type. A matrix plate has similar functionality to a box, where the containers inside can be moved around and removed altogether.

Plates are all associated with schemas, which define the type of the plate (e.g. "96 Well Plate") along with the fields that are tracked, the dimensions of the plate, and whether or not the plate is a matrix plate or a traditional well plate.

Like all inventory, every Plate has a barcode that is unique across the registry.

List printers.

Manage project objects.

Manage registry objects.

See our documentation on how to register entities.

Requests allow scientists and teams to collaborate around experimental assays and workflows.

RNA Oligos are short linear RNA sequences that can be attached as primers to full DNA sequences. Just like other entities, they support schemas, tags, and aliases.

Chains of linear, single stranded RNA that support most capabilities and attributes of DNA Sequences.

Schemas represent custom configuration of objects in Benchling. See this guide in our documentation on how Schemas impact our developers

Endpoints that perform expensive computations launch long-running tasks. These endpoints return the task ID (a UUID) in the response body.

After launching a task, periodically invoke the Get a task endpoint with the task UUID (e.g., every 10 seconds), until the status is no longer RUNNING.

You can access a task for up to 30 minutes after its completion, after which its data will no longer be available.

View team objects.

Manage user objects.

Manage warehouse credentials.

Workflow flowchart config versions are versioned graphs of flowchart configurations.

Workflow flowcharts represent the nodes and edges that a flowchart is comprised of.

Workflow outputs are outputs of a workflow task

Workflow task groups are groups of workflow tasks of the same schema

Workflow tasks encapsulate a single unit of work