Table of Contents

Sample Manager Overview
   Get Started with Sample Manager
   Tutorial: Learn Sample Manager
     Tutorial: Add Samples
     Tutorial: Define Assays
     Tutorial: Add Users and Assign Roles
     Tutorial: Outline Workflow
     Tutorial: Track Sample Sources
   Sample Manager Dashboard
   My Account
   Release Notes - Sample Manager
   Sample Manager - FAQ

Sample Manager Overview

LabKey Sample Manager helps you efficiently manage your laboratory workflows. The intuitive interface makes it easy to:

Explore LabKey Sample Manager. See what a working system looks like in our read-only example project:

You can take a guided tour through this Sample Manager example project by following this topic:


To return to this documentation from within the application, select Help from the user menu.

More Answers

Get Started with Sample Manager

Welcome to LabKey Sample Manager

This topic will help you get started as an administrator using LabKey Sample Manager for sample tracking. First, complete the tutorial to learn to add sample information, define assays, and create the workflow processes you will follow. When you first create a LabKey Sample Manager project, it will be empty, so these topics are designed to populate each area of the application with tutorial examples.


After completing the tutorial, you can return to this page to follow this sequence to start adding your own data.

Configure Freezers

Matching your physical storage to virtual storage locations in the app can make it easy to know where to find the samples you need.

Add Sample Inventories

Getting your sample information loaded is the heart of using Sample Manager. Define the structure of the data to describe each "type" of sample in your system. Once the types are defined, the samples can be created within the application or via spreadsheet import.

Associate Sources

If your samples have physical or biological sources that you want to track, you can learn about adding them and associating them with samples in these topics:

Define Assays

The data you obtain from running instrument tests on your samples will be uploaded as an assay to LabKey Sample Manager. These topics will guide you in designing assays and uploading your data.

Outline Workflow

Your laboratory workflow can be managed by creating workflow jobs for the sequences of tasks your team performs. Add your users, set permissions, and organize your jobs and templates following these topics:

Explore More

Now that you understand the basics, you can learn more about real use cases by exploring our read-only example of a LabKey Sample Manager application in active use.

Tutorial: Learn Sample Manager

This topic is under construction.

This tutorial will help an administrator get started with a new, empty Sample Manager project. Users of the system may also find it helpful to read along to understand how the underlying structures are created.

Administrator Tutorial

Learn the tasks of an administrator by adding a few "Tutorial" samples, defining an assay, and creating simple workflow jobs. Define sources for the samples and see how lineage and timeline features will help users manage their data.

These topics will give you a quick introduction to the tools and process before you load your real data.


After completing the tutorial topics, you will have an understanding of how to use Sample Manager for your own data and workflows.

User Tutorial Sections

Users of the Sample Manager application without administrative permissions but with the "Editor" role will perform the following tasks. Portions of the tutorial that are common user tasks are:

Users with the "Reader" role (or higher) will be able to:

Tutorial: Add Samples

Sample Types help you organize samples in your lab and allow you to add fields that help you describe attributes of those samples for easy tracking of data. Each individual Sample has a unique ID and is a member of one Sample Type. This topic assumes you are starting from an "empty" application and walks you through creating a "Tutorial Samples" type and populating it with a set of samples to use in the next steps.

Create a New Sample Type

Create the first Sample Type in the system by clicking the linked word here in the empty Dashboard Insights panel or by selecting Create a sample type from the main menu under Sample Types.

Once one or more Sample Types have been created on your server, you will click the Sample Types heading from the main menu, then select Create > Sample Type.

Define Sample Type Properties

  • Enter the Name: "Tutorial Samples"
  • Replace the default contents of the Naming Pattern box with the following, so that samples of this type will be clearly identified as part of this tutorial:
  • Click Add Parent Alias to tell the system the name of the column where we will include information about parent samples with our data.
    • Enter "ParentSample" as one word to match our spreadsheet.
    • Select "(Current Sample Type)"
  • If you also see a button for Add Source Alias you can ignore it for now.
  • Click the Label Color selector to choose a color to associate with samples of this type. Our images show orange, but you can select any color you like by clicking, entering a hex value, or individual RGB values.
  • Display stored amount in: Select "mL (milliliters)". Notice that a variety of built-in solid and liquid unit measurements are available, as well as "unit" for cases where each sample is tracked independent of volume.
  • Barcodes: Learn more about barcodes in this topic: Generate Barcodes

Define Sample Fields

  • In the field editor:
    • For this tutorial, disregard the blue banner about adding a Unique ID field for barcodes.
    • Enter the name "Project" and leave the default type "Text" selected.
    • Click Add Field to add another row, enter then name "Concentration" and select "Decimal (floating point)" as the data type.
  • Click Finish Creating Sample Type.

You will now see the details page for this new Sample Type and are ready to create your first samples in the system.

Import Samples from File

Once you have defined the Sample Type for your samples, you can import them by typing directly into a grid, bulk entering values, or by importing a spreadsheet of sample information, as used in this tutorial.

  • Download this spreadsheet to use:
  • The "Tutorial Samples" Sample Type is now available on the main menu. Click to open it.
  • Select Create > Tutorial Samples.
  • Click Import Samples from File.
  • Confirm that "Tutorial Samples" is selected as the Sample Type.
  • Drag and drop the "TutorialSamples.xlsx" file into the target area.
  • You will see a preview of the data file as it will populate rows in the type. A unique "Sample ID" will be generated for each line based on the naming pattern we provided.
  • Click Import.
  • When complete, you will see the samples listed.
    • The generated Sample IDs for each row may vary if other samples have already been created on your system.
    • There are a number of additional built-in columns created for you, including but not shown below, the creation date and user.

Learn more about importing samples from a file in this topic: Import Samples from File

Other Ways to Import and Create Samples

You can also add samples in a grid or using bulk insert methods. Learn more in this topic:

View Sample Details

You can view details about your samples by clicking the Sample ID. For example, scroll down and click Tutorial-018.

On the details page, you have 5 tabs with information:

  • Overview: basic details including the values of all sample properties and fields as well as the storage location (if any).
  • Lineage: parentage and source information (Tutorial-018 has both parent and child sample linkages provided in our example file)
  • Assays: all data about this sample
  • Jobs: all jobs that involve this sample
  • Timeline: a history of events for this sample (so far only registration has occurred)
Browse the information on these tabs before continuing to the next tutorial step.

Related Topics

Start Over | Next Step (2 of 5)

Tutorial: Define Assays

Assay Designs describe the structure of assay data you will gather for your samples. Similar to sample types, you define the properties and fields of your experiment data. Assay data will also be mapped to the sample that it is about. In this topic, we define a "Tutorial Assay" and import an example run of data for the "Tutorial Samples" we created in the previous step.

Create Assay Design

  • From the main menu, select Assays > Create an assay design.
    • If any assay designs have already been created, you will not see this link. In that case, click Assays and then select Create > Assay Design.

Define Assay Properties

Assay properties are elements that apply to all runs that use this assay design, i.e. one value is set for all runs.

  • Enter:
    • Name: Tutorial Assay
    • Description: Complete blood count
    • Check both boxes for Editable Runs and Editable Results to give you the most options to explore with this tutorial assay design.

Add Run Fields

Assay run fields are set once for each run that uses this assay design, i.e. one value is set for each run.

  • Click the Run Fields section to open it.
  • Click Manually Define Fields.
  • Click Add Field to add each of the fields shown below and select the Data Type shown:
    • "Date" of type "Date Time"
    • "Instrument" of type "Text"

Add Results Fields

You could also manually add results fields, which will be different for each row of data within a given run, but in this tutorial, we will infer them from an example spreadsheet.

In the assay designer:
  • Click the Results Fields section to open it.
  • Drag and drop the "TutorialAssay_Run1.xlsx" into the target area.
  • The results fields will be inferred from your upload and shown in the panel.
    • Notice that the SampleID field from the example spreadsheet has been inferred to be of type "Sample" automatically. All assay results must map to samples, so if the system could not infer which field contained that mapping, you would have had to assign it yourself.
    • You can make adjustments if needed to the types and names, but for this tutorial accept the defaults.
  • Click Finish Creating Assay Design.

Now that your assay design has been created, you can use it to import the data from the same example spreadsheet.

Import Assay Data

The "TutorialAssay_Run1.xlsx" spreadsheet you already downloaded contains some "Tutorial Assay" data for some of the samples we created in the previous tutorial step.

You can confirm that the expected set of samples already exists by selecting Menu > Tutorial Samples and seeing that "Tutorial-003 through Tutorial-012" already exist. (Hint: Sort by Sample ID or use the to see the second page of samples.)

  • If you navigated away to check samples, reopen your Assay Design page by selecting Tutorial Assay from the main menu.
  • Click Import Data.
  • Enter Run Details:
    • Assay Id: Enter "Run1". If you leave this blank, a run name will be generated for you based on the assay design name and current day and time.
    • Comments are optional.
    • Date: Enter "2019-10-01" or click the field to use the day/time date picker.
    • Instrument: Enter "INS-01"

Upload Results from File

  • In the Results panel, the Upload Files tab is selected by default.
  • Drag and drop the "TutorialAssay_Run1.xlsx" file into the target area.
  • You will see the first three rows of the data file in the preview section.
  • Click Import.

You will see the grid of results. This grid allows you to filter, search, and sort the result data.

Other Ways to Enter Results

The other tabs in the Import Data interface allow you to copy and paste data from a spreadsheet or enter values directly in a grid, individually or in bulk. Learn more in this topic:

Related Topics

Previous Step | Next Step (3 of 5)

Tutorial: Add Users and Assign Roles

Now that we have created some Samples and learned how to describe and import assay data, it's time to add some other users so we can understand how the workflow management tools work in Sample Manager. To do this, we will add a few fake users and assign them different roles. You must have administrator permissions yourself to complete the tasks in this step.

Add Users

  • To add one or more new users, select Administration from the user menu.
  • You'll start on the User Management page, i.e. the Users tab.
  • Click Create.

In the popup:
  • Enter one or more email addresses, each on it's own line for each user you want to create.
    • For this tutorial, create users for
  • Select the desired Role for the users you are creating. For the tutorial, select Reader for now.
  • Uncheck the box to Send notification emails to all new users since these are not real email addresses.
  • Click Create Users.
You will see the new users added to the grid. In the green banner message, you can click view to filter the grid to only the newly added users.

Assign Roles

Once users have been defined, an administrator can assign them one of the three available permission levels:

  • Readers: Have a read-only view of the application.
  • Editors: Have the Readers' access, and can also add new information or edit data related to samples, assays, and jobs.
  • Administrators: Have full control over the application. This includes user management, permission assignments, and creating and editing sample types, assays, and job templates.
  • Reopen user management if you closed it by selecting Administration from the user menu. Click the Permissions section.
  • All our fake users are currently in the Reader role.
  • Click the for the Editors role to open it.
  • Click the Add member dropdown and select "team_lead".
    • Selected users will be shown in the panel for the role as you go.
  • Click Add member again and select "lab_technician".
    • Each time you select a user, the details for that user will be shown on the right.
    • In the image below, the Editor role is being granted to the team lead and lab technician; all three fake users we added are still also members of the Reader role.

Click Save.

View Audit History

This is a good time to mention that all actions in Sample Manager are logged for later use in an audit. The audit logs can be viewed from any tab within the Administration dashboard, and from many other places in the application. Select > View Audit History. The log opens to the section most relevant to where you were when you opened it.

Learn more in this topic: Audit History

Related Topics

Previous Step | Next Step (4 of 5)

Tutorial: Outline Workflow

This topic is under construction for the 21.9 (September 2021) release of Sample Manager. For the previous version of this documentation, click here.

In this step of the tutorial, you will create a simple job and template, helping you understand how to use jobs, tasks, and templates to represent an efficient sample management workflow. Jobs can include a set of samples, direct links to the necessary assays, and notification mechanisms to ensure the right people know about actions that impact their work.

Create a Job with Selected Samples

  • Select "Tutorial Samples" from the Sample Types section of the main menu.
  • Check the boxes to select "Tutorial-018", "Tutorial-019" and "Tutorial-020".
    • We're including some assay data for these specific samples below.
  • Select Jobs > Start a Job with Selected Samples from the menu above the grid.

Job Details and Priority

On the Details tab of the job creation wizard, enter general properties, assignments, priority, and upload any attachments needed:

  • Job Name: "Tutorial Workflow Job"
  • Description: "This is an example job with three tasks"
  • Job owner: Select "team lead" for this tutorial. This is the user who "owns" the overall job completion, not necessarily owns the tasks. Note that if you did not create the fake "team lead" user and assign them the role of "Editor" in the previous step, you won't be able to select them here and can just select yourself.
  • Notify these users: Add users who should get notifications as this job progresses. Select yourself here.
  • Job start and due dates: Use the date picker to select any begin and end dates you like for the job as a whole. Each task can have an individual due date as well.
  • Priority level: Use the pulldown menu to select "Medium".
  • Attachments: For this tutorial, you can ignore this field. In practice, you could upload a protocol document, detailed instructions, label image file, or any other file attachment required for the job.

Define Job Tasks

Click the Tasks tab to define the tasks for this job.

Any job can be composed of several tasks to complete in sequence. You'll see an empty task when you first open the wizard. Click Add Task to add additional tasks.

For each task in your job, enter the necessary details:

  • Name
  • Description
  • Assign to: Select a user from the dropdown
  • Assays to perform: Select one or more assay here
  • Due date: For this specific task
For this tutorial create the following tasks, using Add Task to add the second two tasks, leaving other fields blank.
Task NameAssign toAssays to Perform (if any)
Prepare SamplesYourself 
Run Tutorial Assaylab technicianTutorial Assay
Review Resultsteam lead 

Assign Samples

Click the Input Samples tab to open it. You will see the samples you selected listed on the Included Samples tab.

Finish Creating Job and Template

Before finishing job creation, consider whether you want to make this job available as a template for creating similar future jobs. Creating a template from a job is offered only during initial job creation.

  • Use the dropdown menu option Save as Template and Start Job to create a template and start this job.

In the popup, you will name the template and provide an optional description. For this tutorial, name the template "Tutorial Job Template 1."

  • Click Save Template.
You will see the job overview. Note the tabs along the top edge for viewing Tasks, Samples, Assays, and Files in addition to the Overview.

Complete Job Tasks

Click the Sample Manager logo to return to the home page of the application. You will now see that the Jobs section has begun to grow. Your Queue includes the job you just created (because the first task is assigned to you).

Click the name of the job to open it. On the Overview page, you'll see summary information, including the list of tasks. The current task is assigned to you.

  • Click Complete Current Task to mark it as complete.
In the Status column, you'll now see that the second task, "Run Tutorial Assay" is now "In Progress".

The assay task is assigned to the "lab technician" but as an administrator you have the ability to complete any task in the system. Let's use that power here to illustrate assay data import from within the workflow system.

  • Click the Tasks tab to see more detail about the task. In this view, you have an Import Data button since the task involves importing data to the "Tutorial Assay".
  • Click Import Data.
  • Enter:
    • Assay Id: "Run2"
    • Date: Today's date (click the entry field to use the date picker)
    • Instrument: INS-01
  • Download this example data sheet: TutorialAssay_Run2.xlsx, then drop it into the upload window.
  • You'll see the data preview.
  • Click Import.
  • When complete, you'll see the imported data.

  • To return to the job details page, you can click the bolded word "here" in the green "Successfully created assay run" banner. For this tutorial, navigate as follows to see how task assignment changes your task queue.
    • Click the Sample Manager logo to return to the home page.
    • In the Jobs section, notice that the job is no longer shown in Your Queue because the current task is not assigned to you. To find the job, click Active Jobs.
    • Click the name Tutorial Workflow Job.
  • Click the Assays tab to see the data you just uploaded.
  • Click the Tasks tab to return to task details.
  • You can now click Complete This Task to mark the lab technician's task complete.

View Timeline

Each sample has a record of all activities that happen for it within the system. To see a timeline, select Sample Types > Tutorial Samples from the main menu and locate "Tutorial-020". Click the name to open details about that sample.

Click the Timeline tab to see the event timeline for this sample.

  • You'll see when it was created (registered), when it was added to the job, and when assay data was uploaded for it.
  • You're also shown the current status of the sample on the right, including who last handled it.
  • If you click an event, such as "Assay Data Loaded" you'll see an additional panel on the right which includes details including a link to the run of data you uploaded.

Related Topics

Previous Step | Next Step (5 of 5)

Tutorial: Track Sample Sources

Sources help you track where your samples came from and trace common attributes across sets of samples from the same source. Sources can be:
  • Physical like labs, vendors, locations, studies, etc.
  • Biological like patients, mice, trees, cell lines, etc.
In this tutorial step, we create and populate two kinds of sources, "TutorialLabs" and "Creatures", then associate the tutorial samples we created earlier with some of each. After doing that, we will examine the kinds of detailed information that are available for samples including timeline and lineage.

Create a Source Type

Creating source types is very similar to the creation of sample types covered in the first step of this tutorial.

  • From the main menu, look under Source Types and click Create a source type.
    • Once source types have been created, click Source Types, then select Create > Source Type.
  • Enter:
    • Name: Tutorial Labs
    • Delete the default Naming Pattern that is provided (and ignore the placeholder text). We will provide unique source names when we create them.
  • Click the Fields section to open it.
  • Download this spreadsheet and drop it in the upload area: TutorialLabSources.xlsx
  • You will see the inferred fields.
  • Notice the blue banner informing you that reserved fields were found and are not shown. This refers to the "SourceId" field that is present in the data file and cannot be "defined again."
  • Click Finish Creating Source Type.

You can now select your new source from the Source Types section of the main menu.

Create Sources (Populate a Source Type)

  • Select your Tutorial Labs Source Type from the main menu, if you navigated away.
  • Select Create > Tutorial Labs.
  • Click Import Sources from File.
  • Drag and drop the same "TutorialLabSources.xlsx" spreadsheet into the target area.
  • You'll see a preview of the first three lines.
  • Click Import to import the file and create these sources.

Create and Populate a Second Source Type

Follow the two sections above to create another source type to use for our tutorial samples, in this case a biological one.

  • From the page for the "Tutorial Labs" you just imported, select Create > Source Type.
  • Name this type "Creatures".
  • Delete the Naming Pattern.
  • Download and use this file for inferring the Fields: TutorialCreatures.xlsx
  • Click Finish Creating Source Type.
  • Select Create > Creatures.
  • Click Import Sources From File.
  • Drag and drop the same "TutorialCreatures.xlsx" spreadsheet into the target area.
  • Click Import.

Now you have two Source Types and we can mark the Samples as having come from one or both types of source.

Associate Samples with Sources

When we originally created the "Tutorial Samples" type, we had not defined these sources, and did not include a way to reference them in the Sample Type definition.

We can now use these new sources when using the Create Samples from Grid entry method for new samples, or by directly editing each individual Sample. Learn more in this topic: Associate Samples with Sources.

For this tutorial, we want to add Source information to our existing Samples. To do so, we must modify the Sample Type design to identify the columns where we will import source information, i.e. the source aliases.

  • From the main menu, select the Tutorial Samples Sample Type.
  • Select > Edit Sample Type Design.
  • Click Add Source Alias.
  • Enter the Source Alias "Lab", and select the Tutorial Labs Source Type.
  • Click Add Source Alias again.
  • Enter the Source Alias "Creature" and select the Creatures Source Type.
  • Click Finish Updating Sample Type.

We now will update the samples we created earlier.

  • If any samples are currently selected, click Clear All.
  • Select Create > Tutorial Samples.
  • Click Import Samples from File.
  • Check the box to Update data for existing samples during this file import.
  • Download this file: TutorialSamplesWithSources.xlsx then drop it into the target area.
  • You'll see a preview:
  • Click Import.

The existing samples have now been updated with source information.

View Lineage

As an example, click the Tutorial-020 sample. Click the Lineage tab. You'll see a graphical representation of the creature and lab sources for this sample, as well as child samples 'derived' from it. Click the icon for either source to see more details about it in the panel to the right.

View Timeline

In the previous step, we saw how assay data import is included in the timeline for a sample, open the Timeline tab for the "Tutorial-020" sample to see that the update we just completed was also recorded for this sample. Clicking the timeline event populates the Event Details panel.

Learn more about the timeline here: Sample Timeline


Now that you have learned to use Sample Manager with our tutorial content, you are ready to start loading your own data into the system. Learn more in the documentation for each area:

Previous Step

Sample Manager Dashboard

The home page of the Sample Manager application offers a summary dashboard for getting a quick overview of your project. Return to this dashboard at any time by clicking the LabKey Sample Manager logo in the upper left corner of the page.

Note that on narrower screens, the panels of the dashboard will be stacked vertically in the following order instead of being arranged as shown above.


At a glance, see the jobs and tasks assigned to you in Your Queue. A second tab will show you other Active Jobs. Learn more about jobs and workflow in this section:

Dashboard Insights

See the current status of the system, with several display options. By default, you see the total count of samples of each Sample Type, shaded by the label color you assign.

Select from the leftmost dropdown to show either Sample Count by Sample Type (the default) or Assay Run Count by Assay.

The next menu lets you control the timeframe over which the count of samples or assays is determined. Options:

  • All
  • In the Last Year
  • In the Last Month
  • In the Last Week
  • Today
Use the < and > buttons to step back and forth through the timeframe options.

Learn more about samples in this section:

Recent Assay Data

See the recently uploaded assay data. By default you will see runs from all assays, but you can use the dropdown menu to select any assay defined in the system and see those recent runs. Learn more about assays in this topic:

Related Topics

My Account

Sign In and Out

From within the LabKey Sample Manager application, you can log in and out via the user menu in the upper right.

To sign in, enter your email address and password on the next page, then click Sign In.

When you are logged in, there will be a Sign Out link on the user menu where Sign In was before.

When you are signed out, you will be able to view the contents as a guest user would - you can read but not edit or create anything.

If you are using a hosted trial version of Sample Manager, CAS authentication provides single sign on and will automatically log you back in. Choosing Sign Out will sign you out of the application and you can click Return to Application to log back in.

Session Expiration

If your session expires while you are using LabKey Sample Manager, you will see a notification popup with a button to Reload Page. You will be asked to log in again before completing the action.

The default timeout is 30 minutes of idle time in the browser. Session expiration can also occur if the server restarts in the background.

Similarly, if you log out of LabKey Sample Manager in another browser window, you will be notified of the need to log back in to proceed.

Edit Your Profile

Once logged in, you can manage your account information by selecting Profile from the user menu in the upper right.

Edit User Details

On your profile page, you can edit your display name, as well as your first and last name and description. You cannot edit your email address here; contact your administrator if you need to change your email address.

Upload Avatar

Drag and drop an image into the drop area to use a custom avatar on your profile. The avatar image must have a height and width of at least 256 px. If you upload a rectangular image, it will be cropped to fit the square.

Once you have uploaded an avatar, you can reedit your profile and click Delete Current Avatar to revert to the default.

Change Password

To change your password, click Change Password in the upper right. In the popup, enter your old password, and the new password you want to use twice. Passwords must be at least six characters cannot contain spaces or match your email address. Click Submit to save the new password.

Related Topics

Administrators can manage user accounts and permissions as described in this topic:

Release Notes - Sample Manager

LabKey Sample Manager makes it easy to manage samples, storage, data collection, and workflows in a small or medium size lab environment. Learn more about the features and capabilities of Sample Manager on our website.

This topic details changes and enhancements in each release as a guide to help users track changes.

Release 21.9, September 2021

Release 21.8, August 2021

Release 21.7, July 2021

Release 21.6, June 2021

Release 21.5, May 2021

Release 21.4, April 2021

Release 21.3, March 2021

Release 21.2, February 2021

  • The field editor now includes checkboxes to enable deletion of multiple fields and export of subsets of fields.
  • Background Import:
    • Removal of previous size limits on data import
    • Progress reporting for asynchronous imports
    • In-app Notifications when background imports are complete

Release 21.1, January 2021

  • Freezer Management
    • Match your digital storage to your physical storage
    • Store and locate samples with ease
    • Monitor usage and capacity in graphical dashboards
    • Track volume, freeze/thaw counts, and comments during check in/out events

Release 20.12, December 2020

  • Detailed audit logging now shows only what has changed when data is updated.

Release 20.11, November 2020

Release 20.10, October 2020

  • Integration with BarTender to print labels.

Release 20.9, September 2020

  • A new tutorial is available to help you get started with a new/empty instance of sample manager. Try it here: Tutorial: Learn Sample Manager
  • Label colors are shown in the samples section of the main dashboard.
  • In anticipation of future support for Freezer Management, underlying functionality like the ability to access storage locations from the main menu have been added.

Release 20.8, August 2020

  • Sample Types can have custom Label Color assignments to help users differentiate them. (docs)
  • In anticipation of future support for Freezer Management, underlying functionality like the ability to see the storage location of a sample has been added. These facilities are not yet visible in the application interface.

Release 20.7, July 2020

  • Improved search experience. Filter and refine search results. (docs)

Release 20.6, June 2020

  • Bug fixes and small improvements

Release 20.5, May 2020

  • Use Sample Timelines to track all events involving a given sample.
  • Detailed audit logging has been improved for samples, under the new heading "Sample Timeline Events."
  • Sample Types can be created by inferring fields from a file, or by defining fields manually. Source types offer the same convenience.
  • Editing of sample parents is now available.
  • The definition of Sample Types can now include "Source Alias" columns, similar to parent aliases already available.

Release 20.4, April 2020

  • The creation interface for Sample Types has been merged to a single page showing both properties and fields. This makes it easier to create naming expressions that use fields in your Sample Type.
  • Define Sources for your samples. The source of a sample could be an individual or a cell line or a lab. Tracking metadata about the source of samples, both biological and physical, can unlock new insights.

Release 20.3, March 2020

  • Samples can be added to a workflow job during job creation. You no longer need to start a job after selecting samples of interest, but can add or update the samples directly within the job editing interface.
  • Removing unnecessary fields is easier with an icon shown in the collapsed field view.

February 2020

  • LabKey Sample Manager is Launched!

Sample Manager - FAQ

You can read a detailed overview of Sample Manager, LabKey's sample management software on our website. Other documentation here will help you better understand specific features and options.

This topic provides answers to some commonly asked questions about LabKey Sample Manager.

Data Ownership and Audit

If I store my data in hosted LabKey Sample Manager do I still own the data? If I choose to end my subscription later, will I be able to get it back?

Absolutely. Whether hosted or on premise, you always own your own data. If you stop using Sample Manager, you will receive a full export of all your data.

Will privacy be maintained if I use a hosted Sample Manager application?

Absolutely, the LabKey security model guarantees privacy and security using our role based access model.

However, if you need to store PHI and/or are interested in HIPAA compliant protection of your data, contact us to discuss whether another LabKey product might better meet your compliance needs.

Do samples have an audit trail for chain of custody tracking?

Yes! Every action is tracked in a set of audit logs on a row by row level. Enhanced chain of custody tracking features are available in a Timeline for samples. Learn more in this topic:

Sample Identification

Is the sample ID assigned by the system unique to just one lab? Can they be shared?

Yes, right now because there is a single Sample Manager application serving each lab, if you ask the application to generate sample IDs for you, they will be unique within that single lab. However, letting the system assign sample IDs is not the only option.

If you wanted to share sample information across multiple labs, you could override the automatic assignment option by providing your own unique sample IDs, such as by using a sample manifest. The distinct Sample Manager applications at many lab sites could accept and use these sample IDs that are drawn from a master assignment list ensuring that they are both unique within a single application and unique across multiple locations.

Does Sample Manager handle replicates?

Yes, sample replicates can be identified using custom naming conventions, i.e. S101-1 and S101-2 are replicates of one original sample.

Does Sample Manager track the subject of study, i.e the source of the sample.

Yes, you can identify and track many types of sample Sources within the application. Learn more in this section:

Does Sample Manager support using a barcoding system?

Yes, with the addition of a "UniqueID" column, Sample Manager will generate unique barcodes for samples. These barcodes are read-only, simple, and easy to use. Learn more in this topic:

Sample Manager also supports integration with BarTender for groups to use for printing labels with sample details. Learn more in this topic:

Freezer Management

Does Sample Manager provide a freezer management solution?

Yes! LabKey Sample Manager launched our freezer management solution in January 2021. Design virtual storage to match your physical storage. Easily find samples, or empty space for storing new samples. Track volume and checkin and checkout to support your workflow. Learn more in this section:

Data Structures for Assays and Samples

How do I get my existing sample data into the system?

LabKey Sample Manager is specifically designed to make data import easy. Design the structure of existing data and drag and drop to upload it simply and efficiently. Note that very large uploads may need to be split into batches to upload successfully.

Are the Assays customizable? Can I create my own assays?

Absolutely. Our demos and example project include some possible ways to structure typical assays, but when you define your own, you have complete control over the fields and types of data collected. The only requirement is that assay data needs to provide a column linking to the sample.

Are there predefined templates for data in Sample Manager?

There are no predefined templates. Users have full control of creating data templates for your own needs. During the definition of assays, users have the option to let the application infer fields in the data structure from the columns in a spreadsheet.

What happens if you import assay data but it has a column name that doesn't match?

The assay data import process will read only the "expected" columns from your data. If you have additional columns, they will be ignored. If you have a difference in column naming, you may be able to make use of column aliases to import data from a column of a mismatched name.

When importing data, you will see a preview of the first few rows to aid you in correcting issues or adding aliases.

How does a user know what columns are expected?

The handy Download Template feature gives the user a blank template for what columns are expected. The user can either add their data to this template or simply confirm that they have the correct columns prior to import.

Can I build in customized data integrity checks?

Absolutely. Every field can have data validation performed, such as ensuring correct formats, valid ranges, and other such measures. Coming soon will be a mechanism for controlled vocabularies, i.e. presenting uploading users with pulldown menus of options instead of free text entry fields.

Do you have support for tracking study visits, where multiple samples of different types are collected from one subject at once?

We don't have a built-in mechanism for tracking study visits at this time, but by defining additional custom columns for your sample types, you can track the individual and date of collection for matching. For example, using a required column for study visit, you would capture this information.

What export types are supported?

Currently you can export data as CSV, TSV, and Excel.

Jobs, Tasks, and Templates

Does each workflow job depend on the completion of the previous job? Or can you have multiple jobs underway simultaneously? Can you configure which job is dependent on which other job?

Each workflow job can begin/proceed independently of all other jobs. You can have as many jobs underway simultaneously as you like. If you want to have actions that proceed in a sequence, consider whether these should be defined as tasks within a single larger job, rather than separate jobs.

In the future, we hope to add an administrative option to make a job dependent upon completion of another job, but at present this is not supported. In the meantime, you could also consider having a 'check for previous job completion' task at the start of the job you want to happen 'next'.

Sample Manager and LabKey Server

Can assay results loaded via Sample Manager be linked to LabKey Studies?

Yes, if you are using Sample Manager as part of a Premium Edition of LabKey Server, your application will be running on the same server as your other LabKey projects. After loading assay data into Sample Manager, you can access it via traditional LabKey Server folder management tools and link that data into your study on the same server.

Can Sample Manager make use of assays already defined in my LabKey Server?

Yes, if you have defined Standard Assays in the scope available to your integrated Sample Manager application, you will see them in the list of assay designs. You may need to map one of the columns to your sample information before you can use them.

Future Plans

We are very interested in hearing your feedback about what is important to you. Future development of new features for LabKey Sample Manager is already underway.

Do you need other software to do data analysis and generate reports?

Yes, at this time, users of the hosted Sample Manager application will export the managed sample data for analysis and reporting. In the future, analysis and reporting will be added within the application.

Note that LabKey Server itself is a candidate for such analysis and reporting, and in fact, users of Premium Editions of LabKey Server can access data from Sample Manager directly from the traditional LabKey user interface.

Does Sample Manager track reagents, vendor batch number, etc.?

Not explicitly at this time. You can use custom columns to track this information yourself. In the future, using controlled vocabularies will give another way to track reagents and their batches.

Related Topics

More Questions?

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