Introduction: 

This walkthrough will go over how to set up your Sample Tracking system and how to configure and create locations, containers, boxes, and plates.

The guide will then go over how to fill these newly containers with your biological samples for effective sample tracking.

Configuration

After the Sample Tracking configuration has been set up for your organization, you can configure your sample management schemas.

  • Navigate to the Registry Settings page by clicking on the gearbox icon in the Registry menu (The sample management configuration occurs in this page).
  • Select the location schema that you want to configure from the left side of the Registry Settings menu.

Locations Schemas

The location schema describe any large storage locations such as freezers, fridges, and or shelves that would house the boxes or plates.

  • Any number of nested locations can be created within the sample management system.
  • Location hierarchy is NOT specified during the initial configuration in the Registry Settings.
  • Location hierarchy is established when CREATING the actual location in your organization's Registry.

To configure a configure a location schema:

  • Select the Create button in the top right corner of the page to create a new location.
  • The location prefix is used to generate a barcode that refers to that location
  • Note: Locations support metadata if desired - e.g. if you have a Temperature field on the Freezer location type.

Container Schemas

Containers schemas describe any type of container (ex. cryovials, eppendorf tubes, and etc.) that directly houses the biological entity/compound. This schema usually gets nested inside the a Box schema.

  • Navigate to the Container Schemas tab in the registry settings.
  • Create a new container type by selecting the Create button in the top right corner of the page.
  • For each container type, specify a name, prefix, and any additional metadata fields the container should track.
  • Note: Benchling will track the contents, volume, concentration, and location fields of the entity/batch in the container - this data is tied to the container itself.

Box Schema

Box schemas are used to describe any type of rectangular, storage box.

  • Navigate to the Box Schemas tab in the registry settings.
  • Specify a name and prefix for the box type (you may also specify additional metadata fields if desired).
  • If you want your boxes to be container agnostic, do NOT select a container type in the drop down menu.

Note: If you want the box to be restricted to a certain container type, you may specify that the box can only hold a specific container schema (e.g. cryovials). 

Plate Schemas

Plates Schemas describe any plate-based storage item (ex. micro-plates, cell-culture plates, and etc.).

  • Navigate to the Plate Schemas tab in the registry settings.
  • Specify a name for the plate type, a prefix, and any additional metadata fields if desired.
  • Additionally, make sure to specify either the Well or the Matrix Vial container option for Fixed and Matrix Plates respectively.

Creating Storage Locations in the Bioregistry

Locations

Once your location schema configurations are completed, you can then create your locations in the Bioregistry. It is best practice to create the locations in a top-down order (location box containers/plates).

Note: Only users with admin level permissions can create “locations” in Benchling.

  • Open your Bioregistry
  • Click into the Storage section.
  • Select the “+” option and then select Location → Create Location.

Note: top-level locations (e.g. a building or lab) do not fill out the Location to Store In field.

  • Select the location type you would like to create
  • Select a name for your location.
  • Select whether you'd like to manually enter a specific barcode, or whether you'd like Benchling to generate one for you.

Note: For top-level locations (e.g. a building or lab where everything can be found), do not fill out the Location to Store In field.

  • If you want to nest locations, (e.g. a freezer in a room), repeat the steps above, but fill out the Location to Store In field with the location schema you want it to be stored. 
  • Repeat this process to create as many nested layers as desired.

Note: Giving these locations a name is completely optional. If you do not enter a name in the Name field, Benchling will use the auto-generated barcode as the name.

Boxes

Once the location hierarchies are created in Benchling, you can begin to create new Boxes.

1). Single Box Creation:

  • Click into the Storage section of the registry and select the “+” button → Create Box.
  • Choose the Box type you would like to create and then search for the location you'd like to store the box within.
  • Choose the name for your box (if no name is specified Benchling will use the barcode as the name).
  • Fill out the Project field if you want control access to this box with specific project's permissions.
  • Click the Create button.

Note: If the Project field was note filled out at creation, access controls can be implemented at a later date.

2). Bulk Box Creation:

You can also bulk import boxes via a spreadsheet and Benchling's data importer.

  • Click into the Storage section of the registry and select the “+” button
  • Select the Box tab → Import Boxes.
  • The spreadsheet only requires 1 column to list the barcode of the parent location where the boxes should be created and stored. 

Note: If this is the only field that is specified, Benchling will auto-generate a new Box (and assign that Box a barcode) for each row in the spreadsheet.

  • If you would like to use your own barcodes, include a second Box Barcode column in your spreadsheet (make sure to map the "box barcode" column in the spreadsheet to the "barcode" field in Benchling).
  • You can also specify a "box name" or additional metadata fields in your spreadsheet.

Containers

Creating containers is an integral part of this process, as all sample entities/batches must be stored in a container.

1). Creating containers:
First create empty containers and assign these containers to a specific location.

  • Open the Storage section of the registry and select the “+” button, choose Container → Import Containers.
  • Select the Container schema to be imported. 
  • Fill out the Project field if you want to set permissions on who can read/write over these containers.
  • If a Project is not specified, then the storage items default to the same permissions as its registry.
  • Transfer the container information from the spreadsheet into Benchling's data importer.

The spreadsheet should contain:

  1. A column for the Box (or Location) barcode where the containers should be stored.
  2. A column for the position (e.g. A1, A2, and etc.) within the Box where the container should occupy.

2). Filling empty containers:

Afterwards, we will fill these newly-created empty containers with registered batch samples using a spreadsheet.

  • Batch samples must exist before being transferred into their containers (preferably, these entities and batches have also been registered).
  • To fill containers, open the Storage section of the Bioregistry and select “+” → Import Transfer Data.
  • Open the spreadsheet containing the batch information to be transferred into the containers.

The spreadsheet should contain these fields (see example below):

  • The ID of the sample batch (Batch ID) that will be transferred into the container.
  • The volume AND volume units of the sample batch to be transferred.
  • The concentration AND concentration units of the sample batch to be transferred.
  • The barcode of the destination container.
  • Copy the information into Benchling's data importer and press Next.
  • Verify that the column names and column types match up.
  • Press Next to transfer samples batches into their respective containers.

Once inside their containers, you can look up their sample information by clicking into the wells of the box and subsequently clicking into the highlighted container.

UI Container Creation:
Alternatively, containers can be created through Benchling's UI once the boxes are set up.

  • Once Boxes are set up, containers can also be quickly created from the UI.
  • Open a registered entity.
  • Click into a Batch on that entity.
  • Click the “+” button next to the Containers list.
  • Fill out the “Create Containers” form.

Plates

Plates are created very similarly to boxes. 

Plates and their housed samples can be created in bulk by using a spreadsheet and Benchling's data importer. 

  • Plates can be created by opening the Storage Section of the registry and selecting “+” → Create Plate.
  • In the screen that appears, select the plate type you'd like to create in the Schema dropdown.
  • Specify a location to store the plate.
  • After a plate has been created, you can use a spreadsheet to fill the plate with material by selecting Import Transfer Data under the “+” menu (in the Storage section of the registry).

The spreadsheet should contain columns for:

  • The batch ID to be transferred into the plate.
  • The volume AND volume units to be transferred.
  • The concentration AND concentration units to be transferred.
  • The barcode of the destination plate.
  • The destination wells in the plate (e.g. A1, A2, and etc.).

Note: you do not need to specify a plate name, Benchling will auto-generate a barcode for it.

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