Core LIMS Training: Project Management

1. Core LIMS Training: Project Management

2. Course Topics • Managing Projects • Workflows • Messages • Queues • Monitoring Workflow Progress

3. Projects • Projects are typically centered around a biological target with a clinical indication • All records in the LIMS are associated to one or more project(s) (default is the General project) • Project managers or administrators can create projects in Core LIMS • Other users will associate experiments, assays, samples, etc. to those projects as the data is entered • Administrators can configure the system to limit users to only view objects from projects that they are assigned to (see Administrative slides)

4. How Do I Start a New Project? 1) Select Project & Workflow Management under the System Menu 2) Select Create under the Projects > Project Menu (Tip: Select List All or Query to view an already existing project) 3) Type in a descriptive name 4) Select the Create New button

5. Reports From the Project Details Page List of Assays that have been associated to the project List of Experiments that have been associated to the project List of Workflows for a project Progress of items in the workflows List of Samples that have been associated to the project Sample, Experiment, Assay reports are useful to get a high level view of how the project is progressing

6. Attaching Project-Level Files • Files that are related to a specific sample or an experiment should be attached to those records • At the project record level, you can attach presentations, SAR tables, background literature, or other documents that span the whole project to share with colleagues 1) Select either Files link 4) Browse to the file 5) Choose the project 6) Select the Upload button 2) Choose the type of file 3) Select the Submit button

7. Workflows • Workflows are a set of rules for automated actions to occur when defined criteria are met • Actions can be sending an automated e-mail alert or adding samples into a queue • Workflows are defined for a specific project • There may be more than one workflow per project • Workflows are intended to 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

8. How Do I Create a Workflow? 1) Select Project & Workflow Management under the System Menu 2) Select Create under the Workflows Menu for the desired workflow type (Tip: Select List All to view/edit an already existing workflow)

9. How Do I Create a Workflow? 3) Type a Descriptive Name 4) Select what type of object(s) will 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

10. Defining the Workflow Steps 1) Click the Add button 2) Click on Add Criteria

11. 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) 1) Choose a numerical 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! 5) Select the Update Criteria button at the bottom

12. 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 Go to Add Actions to define what happens when a criteria is met

13. Adding Actions 1) Check the desired action (you can have more than one) 2) Click the Update Actions button

14. Adding 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 evaluations and actions or to split objects into 2 groups with different actions 1) Type in a new step number(2) 2) Click the Add button 3) Add Criteria and Actions as before

15. How Do Workflows Work? • On the Core server there is a ProjectDaemon tool that is constantly monitoring the system for any new activity (Note: you can check to make sure this tool is still running if the server machine is rebooted – use the Check Project Daemon Status menu option) • When new experiments are published or molecules are registered, the ProjectDaemon evaluates the records to see if they meet the criteria set in the workflows and performs any required actions • Unless it is specifically configured that way, records that are edited are NOT re-evaluated after changes are made

16. How Do I Turn a Workflow Off? The easy way is to click on the Edit icon in the Action Toolbar and deselect the Active checkbox for the Workflow record Another way is to click on the Edit icon in the Actions section and select the Remove checkboxes in the Existing Actions section

17. Messages • Messages are e-mail alerts that can be sent to specific employees when a new record meets a criteria specified in a workflow (they are an “Action” of a workflow) • Common examples of messages are: • New Compound Registered • New Experiment Published • Active Compound Alert • New Task in a Queue • Task in Queue Completed • Each message has it’s own distribution list that project managers or administrators can define – it does not automatically send e-mails to every employee associated to a project

18. How Do I Make a Message Record? Although most messages are hard-coded and you can’t currently customize them on your own, you do need to create a message record in order to tell the LIMS who to send a message to Each group of users that needs to receive a certain message type = one message record 1) Select Project & Workflows Management under the System Menu 2) Select Create under the Messages Menu for the desired messages type (Tip: Select List All to view an already existing message)

19. How Do I Make a Message Record? 1) Choose a descriptive name 2) Select a project 3) Click on the Create New button Note: The Implementation Class should have a default value containing a generic hard-coded message. You can enter a different class with a customized message encoded.

20. Defining Message Recipients Tip: Common e-mail tools (like Outlook) can be configured to set up rules for e-mails to automatically be delivered to a folder if you want to have the information, but do not want an immediate distraction in your general Inbox Check the box and click Remove to take someone off a distribution list The message creator gets a message by default Once the Message record is created, add e-mail recipients one at a time via the pull-down menu Note: the users need to have a valid e-mail address in your domain entered in their Core employee record Administrators: Don’t forget to add Core globally to your trusted senders list so the messages pass SPAM filters

21. Queues • A queue is a way for employees who service multiple users and/or many projects to organize and prioritize tasks • Common examples of queues • Sample requests for inventory group • Requests for assays to be run on specific samples • Requests to synthesize new compounds • Requests to synthesize more material for testing • Queues can be linked to assays if they are related to tasks involving assays

22. How Do I Make an Unlinked Queue? • Limited users (like Administrators or Project Managers) can make a new Queue • All users can add requests to the Queue • Limited users (like Inventory managers or biologists) can complete tasks in the Queue 1) Select Project & Workflows Management under the System Menu 2) Select Create under the Queues Menu for the desired queues type (Tip: Select List All to view an already existing queue) • Which Queue type to use? • Prioritization Queues will be listed in the ‘Add to Queue’ section on the List Functions page • Sample Request Queues will be listed on the ‘Sample Request’ section on the List Functions page

23. How Do I Make an Unlinked Queue? 1) Create a descriptive name 2) Select a project(s) (Use the control key to select multiple projects) 3) Click the Create New button

24. How Do I Make a Queue Linked to an Assay? Select List All under the Assays menu for the desired assay type Select the Queue hyperlink for the desired assay • Click the here hyperlink to create the queue with a link to the current assay • The name and project will be inherited from the assay

25. Ways to Add Objects to Queues • Automatically • Samples that pass workflow criteria will be automatically added to pre-defined queues • Performed by Project Daemon • Useful for saving time for routine decisions • Manually • Users can decide any interesting samples to test • Users will enter the added samples • Sample/Lot/Containers Details page – requester can add 1 object • List Functions page – requester can add many objects • Queue Details page – fulfiller can add many objects • Useful for passing through compounds that are outliers or following up on a scientist’s intuition

26. Requesters Can Add A Sample From Sample Details Queue link will show status of all task requests Users can enter new requests with Add to Queue button

27. Requesters Can Add Many Samples From List Functions You can either transfer hits from a query or go directly to the List Functions page and paste a list of samples that you want to add to a queue The Add to Queue section will add compounds to Prioritization Queues The Sample Request section will add compounds to Sample Request Queues Don’t forget to select a radio button and click on Submit to start

28. How Do I Find My Task List? 1) Select Project & Workflows Management under the System Menu 2) Select List All under the Queues Menu for the desired queues type 3) Clickon the Hyperlink that names your desired Queue

29. Queue Details Page Shows Open Tasks Requests from all users are consolidated into one list Oldest, highest priority items are at the top of the list Easy to send samples to List Functions to process various tasks Can change priority and add comments to requesters Fulfiller can add more objects to the list (from verbal requests, e-mails, etc.)

30. Fulfilling Requests When a request is completed, select the checkbox in the Remove column and hit the Update Queue Members button The LIMS will record the user and timestamp when the task is finished. The page will refresh and remove the completed tasks from view.

31. Viewing Completed Tasks Click on View History to see completed tasks. Click on View Members to return to current open tasks. Turn around time is displayed Click on Cal hyperlinks or type dates in text boxes to change date range (default is 2 weeks) Don’t forget to hit Refresh button to update page!

32. How Do I Monitor Workflow Progress? From any Workflow Details page, click on the Workflow Progress Report hyperlink to get details of what the bottlenecks are

33. Workflow Progress Report Choose a date range to monitor View how many compounds are at each stage of a workflow Click on hyperlinks to get the details of which compounds are at that stage

34. Hands-On Practice In a TEST system (don’t use your production environment, if possible), • Create a new project • Define a new workflow (add criteria and actions) • Create a new message and add an e-mail distribution list • Add some molecules to a Prioritization Queue • Mark some compounds as fulfilled