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Modeling Workflows

Goals

  • Understand what Workflows are and when they are used.

  • Understand design considerations and best practices for modeling Workflows.

  • Know how to create new Workflows using:

    • Protocol Library

    • Sample Sets

    • Data Links

Key Terms

Table 19. 

Term 

Definition 

Workflow

Ordered collection of Protocols, representing a discrete unit of operation.

Protocol Library

List of all Protocols registered in the system.

Sample Set

Entities processed in a Protocol.

Data Link

Pull external and upstream data into a Protocol from the same Workflow or an upstream Workflow in the Workflow Chain.



What are Workflows?

Workflows are an ordered collection of Protocols, and represent the smallest business unit that can be submitted to an Experiment.

master_what_are_workflows_3_3.png

How to model Workflows

Workflows are created to process a group of Protocols that are executed as a discrete unit of operation.

When to create a new Workflow:

  • Discrete units of operation.

  • Branching in the business process.

  • Entity hand-offs (intradepartmental).

    • Provenance should capture who executed the Experiment, and the details of that Experiment.

  • Experimental stopping points.

    • Important when tracking operational metrics like turnaround time.

  • Changes in Experimental throughput.

    • Pooling Entities from multiple Experiments into a single Worksheet (e.g., Library Prep → Sequencing).

Design considerations:

  • How will Experiments be named using this Workflow?

    • What sequence format should be used to name these Experiments?

  • What type of Entities can be submitted to this Workflow?

  • Who should have access to this Workflow?

  • What version(s) should End Users have access to?

  • What Entities are being processed in each Protocol?

  • Are there external data dependencies in any of the Protocols?

How to create new Workflows

Go to: L7|Master → Workflows → + New Workflow

master_new_workflow_3_3.png

Workflow Details

master_workflow_details_3_3.png

  • Use in manufacturing – should be set to “No” for Workflows that will be used in L7 LIMS.

  • Duration (hours) – the time it takes to complete each Protocol in the Workflow.

    • This detail, and the color next to Display Name, is used in L7 Scheduling.

  • Version – a new version of the Workflow is created each time it is saved.

    • Pin – locks the Workflow into a previously saved version for explicit use in Workflow Chains.

Warning

Workflow-level instructions are not supported in L7 LIMS.

  • Experiment Name Sequence – custom name that can be assigned to a newly created Experiment for the selected Workflow or Workflow Chain if the Workflow is the starting node.

    • NONE:

      • User always specifies the Experiment name.

    • Sequence selected but not the “only use sequence for new experiment names” checkbox:

      • User has the option to auto generate or manually specify the Experiment name.

    • Sequence and the checkbox selected:

      • L7|ESP auto generates the Experiment name.

Note

Experiment ID Sequences are added to id_sequences → experiment in the esp Configuration.

Refer to Configuring ID Sequences for more information.

  • Entity Types – restricts the Entities, by type, that can be submitted to an instance of this Workflow. These are the existing Entities or new Entities that can be added when creating a new Experiment.

  • Workgroups – restricts who has access to the Workflow in L7|Master and L7 Projects.

  • Custom Icon – assigns the Workflow an icon in the Workflow Chain builder.

Protocol Library

The Protocol Library displays all Protocols registered in the system. Once a Protocol has been added to the Workflow, it will appear grayed out in the Library.

Using the Protocol Library, you can:

  • Create new Protocols (+ Create New Protocol)

  • Edit existing Protocols by selecting a Protocol in the Library.

  • Construct the Workflow by selecting a Protocol from the Library, then drag and drop it into the main viewing window. As additional Protocols are added, you can rearrange their order by dragging them to a new position (an arrow with a green + sign will indicate the new placement).

    • Select the version of the Protocol. By default, the latest version will be used, but all pinned versions will also be available.

    • Select remove or drag and drop Protocols back into the Library to remove them from the Workflow.

master_add_protocol_to_workflow_3_3.png

Note

The same Protocol cannot be used more than once in a Workflow. However, Protocols can be duplicated in the Protocol builder by expanding the Save menu and selecting Save As.

Note

Workflows cannot start with a Sample Protocol. L7|ESP assumes that the Entities submitted or transitioned to an Experiment are the same Entities in the first Protocol of the Workflow.

Sample Sets

Each Protocol in the Workflow is assigned a Sample Set - the Entities processed in that Protocol.

The first Sample Set is the collection of Entities submitted/transitioned to the Workflow. New Sample Sets are introduced with Sample Protocols. This new, or existing Sample Sets in the Workflow, can be assigned to downstream Protocols in the Workflow. This dynamic feature allows the End User to process more than one (1) set of Entities in the same Workflow, streamlining the business process.

In the absence of a Sample Protocol, every Protocol in the Workflow will use the same Sample Set.

master_workflow_sample_sets__2__3_3.png
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