1. Project Management: Workflows
Core LIMS Training:
Project Management: Workflows
Welcome to CORE LIMS Training. This is the last lesson within the Project Management chapter and will focus on Workflows and how they are configured and used within CORE LIMS. Click on the page when you are ready to begin.

2. Agenda What Are Workflows? How Do I Create a Workflow?
Defining Workflow Steps
Adding Workflow Criteria
Adding Actions
Workflow Progress Report
How do Workflows Work?
Project Jobs
Job Scheduler Page
Turning off a Workflow
This lesson will provide an overall introduction on what Workflows are, how they are created, and how their progress can be monitored through a Progress Report. Project Jobs will also be introduced in regards to how they relate to workflows, and how project jobs can stopped and started within the scheduler page.
To learn more about workflows and how they help to automate standard processes in lab continue on with the lessson.
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3. What Are Workflows?
Workflows are a set of rules for automated actions to occur when defined criteria are met
Actions can send an automated alert or can add samples to a queue
Workflows mimic standard processes done by project team members to save time
Setting up an automated workflow does not prevent users from manually performing the same processes
There may be more than one workflow per project
So what are workflows in CORE LIMS? In the LIMS, a workflow is a sequence of connected steps with rules that move objects automatically through a logical or physical process. Workflows can automate routine tasks like alerting employees when new work needs to be done or moving samples into queues. If your business process has easily definable rules about what conditions need to be met in order to run the next experiment and experiments are run in a specific order, then you will probably save some time by automating some of those processes in a LIMS workflow. Don’t worry, your scientists can always manually run their processes even if they do not meet the criteria defined in the automated workflow.
Typically, a LIMS workflow mirrors the work process for a business project and it is common to have 1 workflow for each LIMS project. However, there is no limit to the number of workflows a LIMS project can have.
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4. What is Your Business Workflow?
Samples are registered
Sample OK to Test? Y
Scientist
Run Assay 1
Sample Active? Y
Run Assay 2
Manager
Let’s take a look at a generic business process. You can see there are certain actions that occur after various decision points. Decision points contain evaluation criteria that filter which objects may pass through the decision point.
A LIMS workflow works in a similar way. However, instead of a person performing the evaluation and pushing the object over to the next task, the LIMS has a job running that keeps constant watch for new things to evaluate and performing the tasks that are defined by rules entered by your LIMS administrator.
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5. How Do I Create a Workflow?
Select Project and Workflows Management under the Application Menu
Select Create under the Workflows Menu for the desired Workflow type
(Tip: Select List All to view/edit an already existing workflow)
How do we define your business process in the LIMS? Workflows are typically configured by an Administrator or Project Manager. They are typically not configured often, unless you have added a new business process that you wish to automate.
To begin creation, navigate to the Project and Workflow Management application. Locate the Workflow Menu Option and click on it to expand. Click on Create submenu to open the Create New Workflow page.
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6. How Do I Create a Workflow?
3) Type a Descriptive Name
4) Select the types of object(s) to be evaluated to see if it meets certain criteria for an action (use the Control Key to select multiple objects)
5) Select a Project
6) Click the Create New button
There are not many attributes to enter when creating a workflow.
The Name field is first. This can be left blank and the system will automatically create a name for you, however, its advisable to create a descriptive name that will help identify the name, according to what the workflow will do.
The Eligible Entity Types fields next, and is required, as indicated by the asterisk. For this attribute, select all of the object types that will be evaluated by the workflow. Hold down the shift or control key to select more than one item at a time. Note that if you select a sample type, the sample lot will automatically show as criteria options - you do not have to select BOTH sample and matching sample lot.
The Project field is the last attribute. If project security has been enabled, it is important to make sure that the workflow is assigned all of the correct projects. This will ensure that users will be able to see all of the appropriate project data. The Projects field is for the Workflow record itself and to define what users will be allowed to view this record if you have Project Security turned on. The Watch These Projects selection is to define which records we will apply our workflow criteria to. For example if you only want samples from a specific project to be evaluated and receive actions, then select that project here.
Click on the Create new button to save your selections.
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7. Defining the Workflow Steps
Click the Add button
2) Click on Add Criteria
After clicking on the Create New button, you will be directed to the Workflow Details Record. This page will let you define all of the workflow steps.
Locate the Add button. Leave the default "1" in the box and click on Add to add a new step. This will add the first step in the workflow, and the first decision point within that step. This indicates the starting point for all objects that enter this workflow. Workflows can contain multiple workflow steps and each step can contain multiple decision points. Decision points contain evaluation criteria that determine if an object can pass on to the next step. We will show how to add more steps and decision points later. For now, let’s add some criteria to our first decision point next.
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8. Defining Criteria
Criteria can be based on assay results (at the top) or the object type(s) that you selected when you created the workflow (on the bottom)
You can set multiple conditions to meet for your criteria (record must meet ALL criteria in a single workflow step to pass – if you want to have a record meet ANY of multiple criteria to pass, then enter criteria in separate workflow steps)
Choose a numerical or Boolean attribute (if all fields are text, your administrator can add a simple numerical attribute that can serve as a flag)
2) Select operator
3) Enter the threshold value that the record must meet
4) Don’t forget to select the checkbox!
Click on the Add Criteria link to see the available Criteria that can be added. The criteria options available will reflect the entity types you selected when the workflow was created in addition to all assay types. You can edit the workflow record now if you want to add more entity types.
Generally speaking the Criteria table will allow you to select an available assay or sample type on the left, select a specific attribute on the right, and then enter a value and an operator to define the rule that will be used as criteria. Note that you are only allowed to use numeric or Boolean attributes as criteria in your workflow. If you only have string attributes for a key assay or sample type, it may be worth adding a simple Boolean attribute to the entity type so that it can be used to pass objects through a workflow.
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5) Select the Update Criteria button at the bottom

9. Reviewing Criteria
Click on the Edit icon in the Criteria section to edit the criteria.
Repeat the same steps to add more criteria for the same action
Go to the top of the page to remove previous criteria
The Edit icon in the Action Toolbar will edit fields relating to the general workflow record, NOT the Criteria or Actions in specific steps
You can change the object types that criteria thresholds can be set for here
Once you save the criteria, you will be returned to the workflow details page to see a summary of your choices. You can edit the criteria at any time by clicking on the Edit button in the Criteria section. (Note that the edit icon in the main toolbar will let you edit general attributes about the workflow like name or eligible entity types).
Now that we have defined which objects will pass the first step of the workflow, we need to define what actions we want to happen to those objects that pass.
Go to Add Actions to define what happens when a criteria is met
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10. Adding Actions Check the desired action (you can have more than one)
Click the Update Actions button
Actions are usually to send messages or add samples to a queue
There are two basic types of actions that can be added to a workflow. You may define one or more actions on any step.
One action you can add is to automatically add objects to a queue. We discussed how queues can organize and manage a scientists’ tasks in an earlier lesson.
The second type of action you can add is to send an messages. We also discussed Messages in an earlier lesson. messages can be used to alert a set of users that new samples are ready for testing in the next assay or that certain samples are particularly active and should be reviewed.
To add an action, click on the Add Actions hyperlink,
The Action Criteria page will provide the Administrator with all of the available Actions that can be used in the workflow. You can select any messages that you want to send. If you have not previously configured any message records, you should review the Messages lesson for more details.
You can also select available queues that you want to add objects to. The LIMS will automatically indicate that records were added by the LIMS automatically from the workflow, but you can fill out any additional comments here. Again, if you have not previously set up queues, you may need to review that lesson so that you have queues to select here.
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11. Adding More Steps
Step 2 criteria will only be evaluated for samples/experiments/etc. that have met the criteria set in Step 1
It is useful to add a second step when you want to have a series of sequential evaluation and actions or to split objects into 2 groups with different actions
Type in a new step number(2)
Click the Add button
Add Criteria and Actions as before
Additional decision points and steps can be added at any time. If we want to add a new workflow step, just enter “2” in the box and click on the Add button.
You can also add multiple decision points for a single step. For example, if we want to add a second decision point for the second step, just enter “2” again and click on the Add button.
You can add the criteria and actions in exactly the same way as we just did for the first step.
You cannot remove decision points or steps after they are added, but if you leave them empty, they will not affect the workflow.
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12. Workflow Progress Report
Workflow Progress Report button will take you to a report that gives you an overall picture of bottlenecks
You can set date ranges
Hyperlinks will let you see which records are in a queue
Back on the Workflow Details page, you will see that there is Workflow Progress Report button. When clicked on, it will provide the user with an overview of where objects are in the workflow and will show exactly how many items are currently at a specific status point of the workflow. This will help users to see if there is an excessive amount of objects at one particular spot that may indicate a bottleneck or issue within the lab. If you click directly on the number link indicated at each status, you will be taken to a view of the exact items within that status.
The report runs off of a date range which can be modified with each run allowing for the ability to see data across various date ranges.
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13. How Do Workflows Work?
Project Job Entity Types monitor the database for new activity and evaluate the criteria defined in the workflow to determine if any objects will pass the criteria
If objects pass workflow criteria Project Job Entity Types trigger the required action on that object
If objects do NOT pass workflow criteria, nothing happens and the object does not continue on with the workflow.
So how do workflows actually work behind the scenes? Project Job Entity Types are configured within the Main Admin Panel, to monitor the database for new activity and to evaluate the criteria defined in the workflow to determine if any objects will pass the criteria. If they do pass the specified criteria, the Project Job Entity Type will then be responsible for triggering the required action on that object.
You can view the Project Jobs from your main admin panel. If you expand the Project Job Entity Type, the LIST ALL action will provide a list of jobs. Two key job records work together in parallel to process workflows.
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14. Project Job Entity Types
PD-ExperimentPublishJob
Evaluates any published experiments to see if those samples now meet any workflow criteria
PD-EntityProjectJob
Evaluates records when they are created or updated to see if they now meet workflow criteria
Each can be selectively turned on/off allowing for greater control aiding in improved system performance
The PD-ExperimentPublishJob is responsible for evaluating any published experiments to see if those samples now meet any workflow criteria.
The PD-EntityProjectJob evaluates records when they are created or updated to see if they now meet workflow criteria.
Splitting the above into separate jobs allows for greater control over job activities because each job can be selectively turned on or off, and the frequency that each job is run can be individually set. This can help improve on the overall system performance.
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15. Job Scheduler Jobs can be De-scheduled and Scheduled as needed
To enable or disable a job, navigate to the Job Menu item and select the Job Scheduler submenu. This will bring you to the Job Scheduler Page. The Job Scheduler Page will show a running log for each job. You will need to refresh this page if you want to view any recent updates to the log.
To turn off a job, simply click on the Deschedule job button located in the Action column in the row for the job name that you want to turn off. Once it has been turned off, the job will be moved to the bottom and will be colored. The corresponding action button will also change to read: Schedule job. Clicking on the Schedule job button will allow you to restart the job when needed.
If you want to stop ALL jobs, you can click on the Deschedule All Jobs button at the top of the page. This will stop all jobs at the same time. If you wish to restart all jobs, click on the Schedule All Jobs, button to start all jobs again.
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16. How Do I Turn a Workflow Off?
The easiest way to turn a workflow off is to click on the Edit icon in the main tool bar and deselect the Active checkbox for the Workflow record
You can also turn off specific actions - click on the Edit icon in the Actions section and select the Remove checkboxes in the Existing Actions section
If you stop a job, remember that you will be stopping a job for all workflows. If you just want to turn off one specific workflow and leave all other workflows running, you can turn off that workflow by editing the workflow record and deactivating the workflow record. You can recheck the Active checkbox later if you want to restart the workflow again.
You can also leave a workflow running and just turn off specific actions. Click on the Edit Icon by the Actions section of the step you want to change. Just deselect any actions you no longer need and save the changes.
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17. Review What Are Workflows? How Do I Create a Workflow?
Defining Workflow Steps
Adding Workflow Criteria
Adding Actions
Workflow Progress Report
How do Workflows Work?
Project Jobs
Job Scheduler Page
Turning off a Workflow
This chapter has provided a brief introduction on what workflows are, how they are created, how they are used within CORE LIMS and how they can be stopped, started and how their general progress can be reviewed. If more in-depth information on workflows is needed, please refer to the documentation
Thank you for taking the time to invest in CORE LIMS Training.
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