This topic shows a few ways to use the Lab Workspace folder we built during the tutorial, extending its functionality. In particular, it shows you how to incorporate freezer locations and sample status information, interlinking related information in a user friendly way.
When you have completed these steps, the Workspace will include the following tables and relationships:
Using the Lab Workspace
Here are some ways you can use the Lab Workspace folder:
Importing New Samples
When new samples arrive at the lab, register/import them on the
Vials tab. You can import them in one of two ways:
- as a new Sample Type by clicking New Sample Type.
- or as new records in an existing Sample Type by clicking the target Sample Type and then clicking Import More Samples.
Each sample must have a unique name. The server enforces unique names for each sample on the server and will not allow you to import two samples with the same name. The easiest way is to provide unique values in the Name (or SampleID) field. There are other options for providing (or generating) sample IDs, described in the topic
Sample Naming Patterns.
Import Assay Results
New assay results can be imported using the
Experiments tab.
- Drag-and-drop any new files into the Files web part.
- Once they have been uploaded, select the new files, click Import Data, and select the target assay design.
Notice the
Usages column in the files web part: Entries here link to the assay design(s) into which the data has been imported. Click to open the result data for that usage.
Discover Which Vial Generated Assay Results
When samples and assay results have been imported, they are automatically linked together (provided that you use the same id values in the Name and SpecimenId fields). To navigate from assay results to the original vial:
- Click the Assay Results tab.
- Then click the assay design (like "Immune Scores").
- If multiple runs are listed, you can:
- Click an Assay ID to see results for a specific run.
- Select one or more rows using the checkboxes, then click Show Results to see a subset of results.
- Click View Results (above the grid) to see all results.
- The SpecimenID field contains links. Each link navigates to a details page describing the original vial.
Inventory Tasks
After
extending the folder as described below, you can use the FreezerInventory grid to query the inventory and answer questions like 'How many samples are in freezer A?'
Extending the Lab Workbook Folder
Here some ways you can extend the functionality of the Lab Workbook folder:
- Add freezer/inventory tracking of the vials.
- Add status tracking for individual vials, such as "In Transit", "Received", "Used", "Ready for Processing", etc.
- Add links from a vial to the results that were generated by it.
Track Freezer/Inventory Locations
This inventory list records the freezer/location of the sample vials. Import the inventory list as follows:
| InventoryID | Freezer | Shelf | Box | RowAndColumn |
|---|
| i-123456 | A | A | C11 | D/2 |
| i-123457 | C | 1 | C12 | E/4 |
| i-123458 | B | B | C4 | A/9 |
- Select (Admin) > Manage Lists.
- On the Available Lists page, click Create New List.
- In the List Designer, enter the Name "FreezerInventory".
- Click the Fields section to open it.
- Drag and drop the "FreezerInventory.xlsx" file into the target area.
- From the Key Field Name dropdown, select InventoryID.
- Scroll down and notice that the Import Data slider is set to import this file when the list is created. (Do not click Import Data or you will disable the data import.)
- Scroll further down and click Save to both create the list and import the data.
You'll see the FreezerInventory added to the available lists. Click the name to see the data in a grid.
Link Plasma to the FreezerInventory
Next you will create a lookup from the Plasma samples to the FreezerInventory list, making it easy to find a vial's location in the lab's freezers.
- Click the Vials tab.
- Click the name of the Plasma sample type, then click Edit Type.
- Click the Fields section to open it.
- In the row for the LocationId field, change the Data Type to Lookup.
- In the Lookup Definition Options set:
- Target Folder: Current folder
- Target Schema: lists
- Target Table: FreezerInventory (String).
- Scroll down and click Save.
- The Plasma samples now link to matching records in the Inventory table.
Note: Any future Sample Types you add can make use of the Inventory table by including a lookup field (such as Barcode or FreezerLocation) as a lookup that points to the Inventory list.
Track Sample Status
Vials have different states throughout a lab workflow: first they are received by the lab, then they are stored somewhere, later they are processed to generate result data. The following list of states is used to track the different events in a vial's life cycle in the lab. The list of status states is not fixed, you can modify it as best fits your lab workflow.
- Download the list: Status.xlsx, which is a list of possible status settings.
- Go to (Admin) > Manage Lists.
- On the Available Lists page, click Create New List.
- In the List Designer, enter the Name "Status".
- Click the Fields section to open it.
- Drag and drop the "Status.xlsx" file into the target area.
- From the Key Field Name dropdown, select Status.
- Scroll down and notice that the Import Data slider is set to import this file when the list is created. (Do not click Import Data or you will disable the data import.)
- Scroll further down and click Save to both create the list and import the data.
Link Plasma to the Status List
Next you will create a lookup from the Plasma samples to the Status list, making it easy to find the vial's state with respect to the basic lab workflow.
- Click the Vials tab.
- Click the Plasma sample type, and click Edit Type.
- Click the Fields section to open it.
- In the row for the Status field, change the Data Type to Lookup.
- In the Lookup Definition Options set:
- Target Folder: Current folder
- Target Schema: lists
- Target Table: Status (String).
- Scroll down and click Save.
- The Plasma samples now link to matching records in the Status table.
Note: Any future sample types you add can make use of the Status table, by adding a lookup field in the same way: by converting an existing field in the sample type to a lookup that points to the Status list.
Improved User Interface
To save yourself clicking through the UI each time you want to see the Plasma samples and the Assay results, you can add these tables directly to the Vials and Assay Results tabs respectively.
To add the Plasma table directly to the Vials tab:
- Click the Vials tab to return to the main tab.
- Enter (Admin) > Page Admin Mode.
- Using the selector on the left, add the web part: Query.
- On the Customize Query page, enter the following:
- Web Part Title: Plasma Samples
- Schema: samples
- Select "Show the contents of a specific query and view."
- Query: Plasma
- Leave other fields at their defaults.
- Click Submit.
Click the
Vials tab to return to the main view. The new panel shows the same grid as you would see if you clicked to the details page for the Plasma sample type.
To add the Assay grid directly to the
Assay Results tab:
- Click the Assay Results tab.
- Using the selector on the left, add the web part: Assay Results.
- On the Customize Assay Results page:
- Assay: select "General: Immune Scores" (it may be selected by default).
- Show button in web part: leave checked.
- Click Submit.
Now the results for the assay are shown directly on the main tab.
- You can now click Exit Admin Mode to hide the tools for adding web parts.
Improve Link from Assay Results to Vial Details
Currently, the SpecimenID field in the "Immune Scores Results" data displays a link to the original vial that generated the data. By default, these links take you to a details page for the vial, for example:
But this is somewhat of a dead end in the application. The problem is that the vial details page does not contain any useful links.
To correct this, we will override the target of the link: we will redirect it to a more useful view of vial details, a details view that includes links into the inventory and status information. In particular, we will link to a filtered view of the Plasma sample type, like this:
- Go to the assay designer view:
- Select (Admin) > Manage Assays.
- In the Assay List click Immune Scores.
- Select Manage Assay Design > Edit assay design.
- Click Results Fields to open the section.
- Click the (expansion) icon for the SpecimenID field.
- Under Name and Linking Options, notice the URL text box.
- By entering URL patterns in this box, you can turn values in the column into links.
- In the URL text box, enter the following URL pattern. This URL pattern filters the sample type table to one selected SpecimenID, referenced by the token ${SpecimenID}.
project-begin.view?pageId=Vials&qwp2.Name~eq=${SpecimenID}
- Scroll down and click Save.
- Test your new link by going to the assay result view:
- Click the Assay Results tab.
- In the Immune Scores Results panel, click a link in the SpecimenID field.
- You will be taken to the Plasma Samples grid filtered to show only the particular specimen you clicked.
- To see the entire Plasma sample type unfiltered again, click the in the filter description.
Congratulations
You have now completed the Lab Workflow Tutorial.
Learn more about using these and similar tools in the topics linked from here:
