Create and execute a legacy Workflow

Legacy Workflows in Benchling provide a structured approach to managing experimental processes, enabling teams to track samples, register entities, and manage transfers seamlessly. While Benchling has introduced updated workflow features, many organizations continue to utilize Legacy Workflows for their established protocols.

This guide offers detailed instructions on executing Legacy Workflows, if you are looking for information on Workflows, see the linked article. 

Overview of legacy Workflows 

A legacy Workflow is a sequence of processes performed to answer a research question or synthesize a new material. Legacy Workflows are powered by legacy Workflow templates that are configured by your team’s admin. These legacy Workflow templates are reusable templates that define an ordered collection of stages and the connections between them. 

In legacy Workflows, each Workflow template corresponds to a stage. A stage is a distinct step in the process that modifies or analyzes a biological entity. The template for each stage defines a default entry that can be used to record results in the stage. 

Each execution of a stage in a legacy Workflow is called a run. The end-to-end set of runs for a single sample is called an arm. 

Create a new legacy Workflow

When you create a new legacy Workflow you are providing all the information about who has permissions to view and edit the Workflow as well as defining where containers and entities that are created will be stored. 

1. Navigate to the legacy Workflow application, then click + New Legacy Workflow
2. This will open a modal where you will need to define the attributes of the workflow. This includes providing a name and folder
3. Use the buttons at the left to select which template you want to use and optionally use the dropdown at the right to select which version of the template you want to use
4. Once you have all the required information filled out, click Create 

Execute a legacy Workflow 

Once you’ve created the legacy Workflow, you have additional things to define before starting the Workflow. Once you’ve started the execution process you will complete runs and update the status of the stage. 

Initialize a legacy Workflow 

To begin executing a legacy Workflow you have the option to edit the stages defined by the template you chose and select the inputs. 

You can add or delete stages, but you can also edit stages by adding experimental conditions which allow you to create an arm for each condition of an experiment you’re running. This might include things like incubation time, temperature, etc. 

Adding inputs allows you to track the origin and context of the materials or entities entering each stage of your Workflow. Inputs also allow Benchling to automatically map relationships between legacy Workflow stages, supporting downstream registration, reporting, and compliance.

1. Optionally make edits to the stages, this includes adding, deleting, or editing the stages in the template
   • Add stages by clicking the + icon in the Edit stages section. This will open a modal where you are required to give the new stage a name and optionally an entry template and experimental conditions before clicking Create stage
   • Delete stages by clicking the delete icon to the right of an individual step. This will open a modal asking you to confirm that you want to delete the stage
   • Edit stages by clicking the edit icon to the right of an individual step. This will open a modal where you can edit the name, entry template, or experimental conditions before clicking Save
     • Add experimental conditions by using the textbox to give the condition a name. Click the + icon to add additional conditions
     • Once you create conditions, use the textbox to define each option you want for a given condition. Click the + icon to add additional options
2. Define the starting material for the legacy Workflow by using the Input Samples search bar to search for an entity
3. To add another input material, click the + icon in the input section and use the search bar to add the next entity. Adding additional entities adds an a new arm to your workflow
   1. Use the + icon to bulk upload inputs from a CSV or spreadsheet
4. When you have finished making edits and designating input(s), click Start Legacy Workflow    

Remember that if you make changes to the stages to tailor your process, these changes will only be reflected in the Workflow you edit. They will not be reflected if you make another legacy Workflow from the same template.  

Split by conditions 

If you set up experimental conditions, you have the option to split a stage into multiple arms based on the condition groups. Splitting by conditions can only be done before you click Start Legacy Workflow.   

1. Go to the diagram of the legacy Workflow and identify a stage with experimental conditions
2. In that stage, right click on the arm you want to split and choose to Split by conditions

Note: the split will only occur for arms in a single stage. If you have multiple stages with experimental conditions, you would need to repeat this for all arms in the subsequent stages. The more you split conditions upstream, the more arms you will have as you proceed through the legacy Workflow. 

Complete a stage in a legacy Workflow

Once you have your legacy Workflow created, you will use the templates in each stage to complete the planned experiment. Once completed, you can update the status of the stage to signal if it is initialized, completed, or discarded. 

1. Click on the name of the Entry in the relevant stage to open it
   1. Each arm will have its own specific entry
2. Complete the instructions in the template, this may include filling out structured tables
   1. For Registration tables, use the Stage Run dropdown to associate the input sample with the new entity that you are creating, fill out and submit the rest of the Registration table as usual
   2. For Inventory tables, use the + icon at the top of the table and click on Add samples which will open a modal allowing you to designate the input samples or any entities registered in the Entry as samples. Fill out and submit the rest of the Inventory table as usual
   3. For Result tables, use the + icon at the top of the table and click on Add samples which will open a modal allowing you to designate the input samples or any entities registered in the Entry as samples. Fill out the rest of the Results table as usual
3. Once you’ve completed the template and the relevant output sample is created, return to the legacy Workflow dashboard to update the stage, you can do this in bulk or for each entry (shown below)
4. Click the ˅ icon next to the entry that you’ve completed, this will open a menu where you will want to navigate through the Update status option to select Completed
5. Repeat this process for each arm and each stage of the legacy Workflow

Note: Output samples automatically populate in the table based on how the legacy Workflow template is configured. Typically they are defined by what structured tables you insert to create and process input entities. These outputs represent newly registered entities or results from the legacy Workflow. You can update the Output Samples table so it reflects containers created in the Entry. 

If a run fails, you can update the status to Discarded instead of completed. This will delete all downstream stage runs and is not reversible. 

Structured tables in legacy Workflows work much the same way they do throughout Benchling, allowing you to pull in structured data from spreadsheets, entity fields, and formulas. 

The options at the top of the table are slightly different: you can print barcodes, re-sync the table, create a legacy request, download the table as a CSV, and toggle settings for name and Registry ID. 

Additional actions you can take while executing a legacy Workflow

While completing a workflow, you may find yourself needing to add or delete stages or take actions on a specific branch. The list of actions below discuss what you can do when this happens and any consequences of these actions. 

Insert a stage 

If you need to add an additional step to an individual workflow that isn’t reflective of a change in the overall process, you can add a stage to the workflow.

1. Click on the ˅ icon next to the stage you want to add a stage after
2. Choose the Insert stage after option from the menu
3. This opens a create stage modal that requires you to provide a name for the stage, an optional entry template if one is already created, and optional experimental conditions
4. Once you’ve included all the information you need for the new stage, click Create stage
5. To add the input samples to the new stage, click on the ˅ icon next to the new stage you’ve created
6. Choose the Add runs inline option from the menu
7. This opens a update stage runs modal that requires you to confirm the Entries for each arm that you are running
8. Once you’ve confirmed everything in the modal, click Create run  

Delete a stage

If you need to remove a step in an individual workflow that isn’t reflective of a change in the overall process, you can delete a stage from the workflow. 

1. Click on the ˅ icon next to the stage you want to delete
2. Choose the Edit stage option from the menu
3. This opens an edit stage modal, click Delete stage
4. Because deleting a stage is permanent and cannot be undone, you will need to click Ok in a second modal to confirm the action 

Add a branch 

If you need to represent that work in one stage is going to be done by two separate people, you can duplicate a branch in that stage to maintain its lineage to the previous run.

1. Right click on the run that needs to be duplicated
2. Choose the Duplicate branch option from the menu
3. Use the Entry dropdown to select the Entry template or set the template to a new Entry
4. Click Create run 

Delete a branch 

You can delete a run or delete a run and everything downstream of it so that the workflow only depicts work that has been done. 

1. Right click on the run that needs to be deleted
2. Choose delete run or delete this and all downstream runs from the menu

Split by inputs 

If you complete a stage and you create more samples than initially planned, you can update the stages after it so that branches are split by the input. 

1. Click on the ˅ icon next to the stage that needs to be split
2. Choose the Split by inputs option from the menu
3. This opens an update stage runs modal that allows you to confirm what Entry templates you want to use for the new runs
4. Click Create runs to confirm and create individual runs for each sample

Pool runs  

During your workflow, you may end up mixing samples that were split at a prior stage, you can adjust a stage in your workflow to reflect this. 

1. Right click on one of the branches
2. Choose the Delete run option from the menu
3. Right click on the remaining branch in the stage that you want to pool
4. Choose the Edit run option from the menu
5. This will open an update stage runs modal
6. In order to pool the branch from the subsequent stage, hold the command key on your keyboard (Control on a PC) while clicking the branch that needs to be added in the stage you are editing. You should see a diagonal line form between that branch and the run in the new stage
7. Once you’ve made all the updates you need, click Edit run