How to fill a plate
Begin with your plate, and select the wells you’d like to fill with entities by clicking on each of the empty circles.
You can highlight multiple wells by selecting one and dragging to include the others
Once the source entity is found via the search under Add sources, you can decide between adding the sources to each well or selecting separate sources and adding them to wells by pattern
Once the source or sources are added, you can specify what quantity should go in each well for each source
You can also add wells via structured table
How to Annotate Plates
This release allows users to annotate and fill assay plates so that they can track the addition of up to 10 entities in a single well of a fixed well plate that has 384 wells or less.
This release allows users to improve their:
Quality - the ability to visually design and annotate wells and save an immutable record of the actions taken on the plate to the Notebook improves the quality of data and tracks its validity
Efficiency - with the ability to fill new or existing plates with multiple entities in the Inventory and Notebook, researchers can design and annotate plates with the interactive wizard in a way that makes sense with how they use the tenant
Speed - with the ability to visualize metadata on the plate entity, they can surface insights about their research faster
Plate maps in Benchling are created by a UI wizard that allow you to visually design and annotate wells in a fixed plate. As you annotate the plate, you take a few key actions including defining well roles and setting schema field values before you add sources and define your transfer. Together these actions allow you to view the metadata of the plate.
The image below is of the plate mapping wizard tool. Click on the directional arrows for more information about the different parts of the wizard.
Well Role
As part of defining the plate map, when you select the Well Role layer, you are able to interact with the wells in the well plate to map to annotate selected wells. As you annotate the plate, you can define the following:
Primary role - the primary role of a well designates whether the well is filled with a sample, control, standard, or blank
Sub role - the sub role of a well is an optional designation for control wells that allows you to add further information about your controls by indicating if they are a positive or negative control or if they are maximum or minimum controls
Numbered groups - numbered groups can be used so that you can more easily visualize the replicates of samples, controls, or standards in the plate. Group numbers can be specified by group or filled in as a pattern. If filling by pattern, you can designate not only the number of replicates but also the direction of the pattern.
You can interact with the plate in different ways outside of clicking on a single well – highlighting a column, dragging across columns, etc. – when defining the well roles.
10 is the limit on the number of schema fields you can annotate in a given plate record
As part of defining the plate map, when you select the Contents layer, you are able to select wells that you’d like to add sources to. To do this, search for containable entities, source containers, or worklists and select how you’d like to see them added to the well.
For a list of sources you can:
Add all sources to each well – where every listed source will be added to every selected well
Add one source to each well by pattern – where every you can define a pattern or use the patterns in the role layer to add a single source to each well
Clear Wells
The clear wells button allows you to clear the role and/or contents of selected wells. In the Contents layer, the clear wells button allows you to remove all sources that have been added to the well, or individual sources that may have been added to a well in error.
Define Transfer
Once you’ve designated well roles and added sources, you have the option to enter information about the transfer of each source into the table. Defining the transfer is an optional step that allows you to capture more information about your experiment. You can fill out as much or as little information here as needed.
In this part of the wizard, you can include the following information:
Source concentration
Transfer quantity
Final concentration
Total well volume
You can define the transfer information for all wells, if volumes and concentrations are applicable across the plate or toggle to a well by well view of the table to insert specific concentrations and volumes.