How to use plate maps

Introduction

Plate maps allow you to design and manage fixed plates with an interactive interface for designing, creating, and visualizing assay plates in Benchling reducing reliance on manual data entry, increasing flexibility in plate based workflows, and surface assay insights faster. The plate mapping tool allows you to annotate wells, fill plates with multiple entities per well, and visualize metadata directly on the plate entity.

This information can be captured with a plate design or a plate record. A plate design enables you to plan your plate layout ahead of experiments so that you can make edits and re-use the plate design again and again for similar assays. A plate record allows you to see an immutable record of what you did to the plate and can be created from a plate design or directly in the plate map.   

The tool is most useful for an analytical workflow where:

• You are designing only one or a few fixed plates (not matrix plates)
• Fixed plates are not larger than 384 wells, or 24 columns and 16 rows 
• You are performing transfers from a list of containers or entity sources to a plate

Inserting a plate map into an Entry

In order to annotate and fill plates in a plate design or plate record, you’ll need to launch the plate map tool from the Notebook. The steps to create a plate design and a plate record are captured below. The steps for annotating and filling the wells are listed further down in the article.  

How to create a plate design 

1. Open a Notebook entry
2. Use the Insert dropdown to select Plate map
3. In the select map type prompt, choose Plate design
4. Provide a name and schema for the plate, then click Next
5. Annotate and/or fill the wells based on your experimental design, for more information see the Annotating well roles and schema field values section
6. When finished, click Save design
7. To edit a plate design once it has been created, click the pencil icon to make any changes to the plate design
   Note: Once you make a plate record from a plate design, you will not be able to edit the plate design 
8.  

How to create a plate record

If you already have a plate design made, click the Fill plate button which will open the modal where you define plate attributes. 

From this point, the steps to create the plate record are the same as if you were inserting just the plate record, which are listed below. 

1. Define if you would like to annotate and fill a new plate or an existing plate 

2. Define the other plate attributes including schema, plate name, project, and the location you’d like to store the plate in, then click Next 
3. Annotate well roles, contents, and schema field values as needed, then click Next 
4. Define the concentration or volume of the transfer for well or entity, then click Fill
   Note: Once a plate record is added, you can update it to add new contents, but you cannot remove contents from a plate 

Annotating well roles and schema field values 

Metadata is captured against wells in two different layers: the Well role layer and the Schema fields layer. The sections below talk about how to add metadata to each layer. 

How to set well roles 

When you select the well role layer, you are able to interact with and annotate the wells in the plate

1. In the plate map tool, navigate to the "well role" layer on the left sidebar
   "Role" is a new system field that can be edited on all wells in fixed plates.
2. Select any wells and annotate selected wells with 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 positive, negative, minimum, or maximum 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.
3. Set values by:
   1. Manually specifying the role and the groups
      Note that if there is only one group (for example, you want all controls to be called “positive control”), you should label them group 1. The number 1 won’t show up on the well if there is only one group.
   2. Filling by pattern, which sets the group numbers for a specific role
      Designate the number of replicates and also the direction of the pattern.

Notice the different ways that you can interact with the plate – clicking single wells, highlighting a column or row, dragging across columns, and more – when defining the well roles.

Fill by pattern follows these rules:

• When fill direction is right, Benchling assigns group numbers starting from the top most cell (on the left)
• When fill direction is right, Benchling assigns group numbers starting from the leftmost cell (at the top)
• Benchling then moves in the fill direction and always starts a new group when a replicate or a row is finished

Setting schema field values 

In addition to roles, Benchling also supports annotating text, dropdown, and number fields on wells.

1. In the left sidebar, toggle to different "layers" of your plate map
2. Select the layer you wish to edit
3. Select wells
4. Set values on wells using the right sidepanel

Users can add or remove schema fields when creating a plate that has valid fields on its container schema. These layers will be shown on the left side of the plate map as seen above. Users can remove layers by hovering over them and clicking on the small x in the top right corner, as shown below. Up to 10 container schema fields can be annotated per plate map.

For more details on configuring plate and container schemas, see Configure box and plate schemas and Configure container schemas. Note that the plate map tool only supports fixed plates and does not support matrix plates.

Saving annotations and viewing metadata on the plate

Once a user has saved edits to their plate, well roles and schema field values are passed to the plate entity. If you open the plate entity, the values set on each well are visible in the plate map and the table on the right. You can toggle between the different layers using the dropdown above the plate map.

Adding contents to wells from source containers or entities 

When you select the Contents layer, you are able to select wells to which you’d like to add sources.

1. In the plate map tool, navigate to the Contents layer on the left sidebar

   "Role" is a new system field that can be edited on all wells in fixed plates

2. Select any wells and use the search bar to find sources — containable entities and containers — to transfer

   1. Typing to search

   2. Adding from a worklist

   3. Adding from a structured table (only if you have launched the plate map tool from a Notebook entry)

3. Once you’ve added sources to the gray box on the right, select the manner in which you’d like to add those sources to the well(s):

   Add all sources to each well – this option adds every listed source (in the highlighted box) to every selected well.
   
   

2. Add one source to each well by pattern – this option allows you to add a single source to each well, either by defining a pattern or using the groupings in the well role layer, as shown below. Using the groups defined for a well role is only available when you select wells that all have the same primary role.

4. Click Add sources to add contents to wells

5. Once you’ve added all sources, click Next to define the transfer 

Note that the plate map tool currently allows you to transfer up to 10 contents per well, and it currently does not support transferring contents with solid units from sources or into wells.

Once sources are added to wells, Benchling will help you visualize the contents you're adding to wells, where contents in the legend are grouped by schema. Hovering over individual wells allows you to see the specific contents in each.

Clearing 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. Note that the options in the dropdown reflect groups of sources, identified by entity schema(s).

Note that you can only clear wells of the contents you had just added within the same wizard. Previously added contents will have to be removed via the “remove contents” button on the plate entity in Inventory.

Defining the transfer

Once you’ve designated well roles and added sources, you have the option to enter information about the transfer of each source. Defining the transfer is an optional step that allows you to capture more information about your experiment; for example, you can track how much volume is decanted from source containers. You can fill out as much or as little information here as needed.

In this part of the tool, you can include the following information:

• Source concentration

• Transfer quantity

• Final concentration

• Total well volume

Source concentration and transfer quantity are properties of the transfer, whereas final concentration and total well volume will set values on the wells of the plate you create.

To set values, edit the transfer table to the right of the plate map. There are two views for this transfer table:

• Summary — This view allows you to set volumes and concentrations in bulk across all wells in the plate, grouping sources by unique combinations of entity schemas

• Well — This view allows you to set volumes and concentrations for individual wells that you have selected in your plate map. You must select at least one well to see and set the values in wells

You can toggle between the two views. If a value is set on the summary view, it overwrites all values on all relevant wells. If different values are set on wells that are grouped together in the summary view, the summary view will communicate that “multiple values” are set on wells.

Benchling will prevent you from making some common mistakes or taking invalid Inventory actions. For example:

• In each well, the sum of transfer volumes for each source must not exceed the total well volume.

• Across all wells, the transfer volume of a source cannot exceed the volume in a source container.

• For each content, its final concentration cannot be greater than its source concentration.

Resolve all errors to finalize the transfer.

Finalizing a transfer and viewing metadata on the plate

After you click “Fill,” Benchling passes metadata to the plate and performs a transfer. The plate entity now contains the contents you filled it with.

If you open the plate entity, the plate map allows you to visualize the contents by schema, and the table includes the contents, their concentrations, and the volume in each well. Well roles and schema field values can also be visualized in both the plate map and the table. You can toggle between the different layers using the dropdown above the plate map.