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
   Release Notes - Sample Manager
   Sample Manager Dashboard
   User Accounts, Groups, and Roles
     My Account
     Permission Roles
     Manage Groups
     Manage Notifications
   Apply Naming Prefix
   Sample Manager - FAQ

Sample Manager Overview

LabKey Sample Manager is an easy-to-use sample management system for any size lab. The intuitive interface makes it easy to track the entire lifecycle of samples in your lab and all associated research data. With the Professional Edition of Sample Manager, you will also be able to:

You can take a guided tour, learn directly from other users describing how they are using the application, and sign up for a personalized demo on our web site:


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 imported from a spreadsheet.

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 (Premium Feature)

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 (Premium Feature)

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:

Use Electronic Lab Notebooks (Premium Feature)

Collaborate and record your work in data-connected Electronic Lab Notebooks. Use templates to create many similar notebooks, and manage individual notebooks through a review and signing process.

Learn more in this section:

Tutorial: Learn Sample Manager

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:
    • You can now hover over the tooltip for the Naming Pattern field to confirm that the pattern has been validated and see an example name that might be generated.
  • 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 amount.
  • Barcodes: Ignore this setting for this tutorial. Learn more about barcodes in this topic: Barcode Fields

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.
  • Click Add, then choose Import from File.
  • You'll be on the Import Samples from File tab.
  • 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 manually, 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 several 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)
  • Aliquots: any aliquots created from this sample
  • 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

Premium Feature — Available in the Professional Edition of Sample Manager. Learn more or contact LabKey.

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
    • Active: Leave this box checked; unchecking it will archive the assay design.
    • 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. You could make adjustments if needed, but for this tutorial just accept all defaults.
    • 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.
    • By default samples of any sample type (i.e. "All Samples") could be uploaded for this assay. If needed you could constrain the lookup to a specific sample type for this specific assay design.
    • 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. As for other grids, you can 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.
  • Click the Users tab to go to the User Management page.
  • 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(s) for the users you are creating. For the tutorial, you can use only the default Reader, or add Storage Editor if you want to experiment with freezer storage actions.
  • 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, with the exception of the storage editor role below. This includes user management, permission assignments, and creating and editing sample types, assays, and job templates.
  • Storage Editors: Storage Editors may read, add, edit, and delete data related to items in storage, picklists, and jobs.
  • Storage Designers: Storage Designers may read, add, edit, and delete data related to storage locations.
  • 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.
  • You may also want to confirm that at least your own user account is assigned the Storage Editor role to explore freezer management features later.
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

Premium Feature — Available in the Professional Edition of Sample Manager. Learn more or contact LabKey.

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.
  • Click the button to open a filter panel.
    • Select SampleID (if it is not selected by default).
    • Check the boxes to select "Tutorial-018", "Tutorial-019" and "Tutorial-020". (We're including some assay data for these specific samples below.)
    • Hint: clicking a name will clear all selections except that one, then add the other two by clicking the boxes.
    • Click Apply.
  • Click the checkbox at the top of the column to select all three.
  • Select Start a New Job from the Jobs menu above the grid. On narrower browsers, this will be a section of the More menu.

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 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 Add > Import 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 Add > Import 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 Add > Import 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

Release Notes - Sample Manager

LabKey Sample Manager makes it easy to manage samples, storage, data collection, and workflows in growing labs across all disciplines.

Learn more about the features and capabilities of Sample Manager on our website.

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

Release 22.11, November 2022

  • Add samples to multiple freezer storage locations in a single step. (docs)
  • Improvements in the Storage Dashboard to show all samples in storage and recent batches added by date. (docs)
  • View all assay results for samples in a tabbed grid displaying multiple sample types. (docs)
  • ELN improvements to make editing and printing easier with a table of contents highlighting all notebook entries and fixed width entry layout.
  • New role available: Workflow Editor, granting the ability to edit workflow jobs.
  • Notebook review can be assigned to a user group, supporting team workload balancing.

Release 22.10, October 2022

  • Use sample ancestors in naming patterns, making it possible to create common name stems based on the history of a sample. (docs)
  • Additional entry points to Sample Finder. Select a source or parent and open all related samples in the Sample Finder. (docs | docs)
  • New role available: Editor without Delete. Users with this role can read, insert, and update information but cannot delete it. (docs)
  • Group management allowing permissions to be managed at the group level instead of always individually. (docs | docs)
  • With the Professional Edition, use assay results as a filter in the sample finder helping you find samples based on characteristics like cell viability. (docs)
  • Assay run properties can be edited in bulk. (docs)

Release 22.9, September 2022

  • Searchable, filterable, standardized user-defined fields on workflow enable teams to create structured requests for work, define important billing codes for projects and eliminate the need for untracked email communication. (docs)
  • Storage grids and sample search results now show multiple tabs for different sample types. With this improvement, you can better understand and work with samples from anywhere in the application. (docs | docs | docs)
  • The leftmost column of sample data, typically the Sample ID, is always shown as you examine wide datasets, making it easy to remember what sample's data you were looking at. (docs)
  • By prohibiting sample deletion when they are referenced in an ELN, Sample Manager helps you further protect the integrity of your data. (docs)
  • Easily capture amendments to signed Notebooks when a discrepancy is detected to ensure the highest quality entries and data capture, tracking the events for integrity. (docs)
  • When exploring a Sample of interest, you can easily find and review any associated notebooks. (docs)

Release 22.8, August 2022

  • Aliquots can have fields that are not inherited from the parent sample. Administrators can control which parent sample fields are inherited and which can be set independently for the sample and aliquot. (docs)
  • Drag within editable grids to quickly populate fields with matching strings or number sequences. (docs)
  • When exporting a multi-tabbed grid to Excel, see sample counts and which view will be used for each tab. (docs)

Release 22.7, July 2022

  • Our user-friendly ELN (Electronic Lab Notebook) is designed to help scientists efficiently document their experiments and collaborate. This data-connected ELN is seamlessly integrated with other laboratory data in the application, including lab samples, assay data and other registered data. (docs)
  • Make manifest creation and reporting easier by exporting sample types across tabs into a multi tabbed spreadsheet. (docs)
  • All users can now create their own named custom view of grids for optimal viewing of the data they care about. Administrators can customize the default view for everyone. (docs)
    • Create a custom view of your data by rearranging, hiding or showing columns, adding filters or sorting data. (docs)
    • With saved custom views, you can view your data in multiple ways depending on what’s useful to you or needed for standardized, exportable reports and downstream analysis. (docs)
    • Customized views of the audit log can be added to give additional insight. (docs)
  • Export data from an 'edit in grid' panel, particularly useful in assay data imports for partially populating a data 'template'. (docs | docs)
  • Newly surfaced Picklists allow individuals and teams to create sharable sample lists for easy shipping manifest creation and capturing a daily work list of samples. (docs)
  • Updated main dashboard providing quick access to notebooks in the Professional Edition of Sample Manager. (docs)
  • Samples can now be renamed in the case of a mistake; all changes are recorded in the audit log and sample ID uniqueness is still required. (docs)
  • The column header row is 'pinned' so that it remains visible as you scroll through your data. (docs)
  • Deleting samples from the system entirely when necessary is now available from more places, including the Samples tab for a Source. (docs)

Release 22.6, June 2022

  • Save time looking for samples and create standard sample reports by saving your Sample Finder searches to access later. (docs)
  • Support for commas in Sample and Source names. (docs)
  • Administrators will see a warning when the number of users approaches the limit for your installation. (docs)

Release 22.5, May 2022

  • Updated grid menus: Sample grids now help you work smarter (not harder) by highlighting actions you can perform on samples and grouping them to make them easier to discover and use. (docs)
  • Revamped grid filtering and enhanced column header options for more intuitive sorting, searching and filtering. (docs)
  • Sort and filter based on 'lineage metadata', bringing ancestor information (Source and Parent details) into sample grids (docs)
  • Rename Source Types and Sample Types to support flexibility as your needs evolve. Names/SampleIDs of existing samples and sources will not be changed. (docs)
  • Descriptions for workflow tasks and jobs can be multi-line when you use Shift-Enter to add a newline. (docs)

Release 22.4, April 2022

  • In the Sample Finder, apply multiple filtering expressions to a given column of a parent or source type. (docs)
  • Download templates from more places, making it easier to import samples, sources, and assay data from files. (docs)

Release 22.3, March 2022

  • Sample Finder: Find samples based on source and parent properties, giving users the flexibility to locate samples based on relationships and lineage details. (docs)
  • Redesigned main dashboard featuring storage information and prioritizing what users use most. (docs)
  • Updated freezer overview panel and dashboards present storage summary details. (docs)
  • Available freezer capacity is shown when navigating freezer hierarchies to store, move, and manage samples. (docs | docs)
  • Storage labels and descriptions give users more ways to identify their samples and storage units. (docs)

Release 22.2, February 2022

  • New Storage Editor and Storage Designer roles, allowing admins to assign different users the ability to manage freezer storage and manage sample and assay definitions. (docs)
    • Note that users with the "Administrator" and "Editor" role no longer have the ability to edit storage information unless they are granted one of these new storage roles.
  • Multiple permission roles can be assigned to a new user at once. (docs)
  • Sample Type Insights panel summarizes storage, status, etc. for all samples of a type. (docs)
  • Sample Status options are shown in a hover legend for easy reference. (docs)
  • When a sample is marked as "Consumed", the user will be prompted to also change it's storage status to "Discarded" (and vice versa). (docs | docs)
  • User-defined barcodes in integer fields can also be included in sample definitions and search-by-barcode results. (docs)
  • Search menu includes quick links to search by barcode or sample ID. (docs)
  • See and set the value of the "genId" counter for naming patterns. (docs)

Release 22.1, January 2022

  • A new Text Choice data type lets admins define a set of expected text values for a field. (docs)
  • Naming patterns will be validated during sample type definition. (docs)
  • Editable grids include visual indication when a field offers dropdown choices. (docs)
  • Add freezer storage units in bulk. (docs)
  • User-defined barcodes can be included in Sample Type definitions as text fields and are scanned when searching samples by barcode. (docs | docs)
  • If any of your Sample Types include samples with only strings of digits as names, these could have overlapped with the "rowIDs" of other samples, producing unintended results or lineages. With this release, such ambiguities will be resolved by assuming that a sample name has been provided. (docs)

Release 21.12, December 2021

  • The Sample Count by Status graph on the main dashboard now shows samples by type (in bars) and status (using color coding). Click through to a grid of the samples represented by each block. (docs)
  • Grids that may display multiple Sample Types, such as picklists, workflow tasks, etc. offer tabs per sample type, plus a consolidated list of all samples. This enables actions such as bulk sample editing from mixed sample-type grids. (picklists | tasks | sources)
  • Improved display of color coded sample status values. (docs)
  • Include a comment when updating storage amounts or freeze/thaw counts. (docs)
  • Workflow tasks involving assays will prepopulate a grid with the samples assigned to the job, simplifying assay data entry. (docs)

Release 21.11, November 2021

  • Archive an assay design so that new data is disallowed, but historic data can be viewed. (docs)
  • Manage sample status, including but not limited to: available, consumed, locked. (docs)
    • An additional reserved field "SampleState" has been added to support this feature. If your existing Sample Types use user defined fields for recording sample status, you will want to migrate to using the new method.
  • Incorporate lineage lookups into sample naming patterns (docs)
  • Assign a prefix to be included in the names of all Samples and Sources created in a given project (docs)
  • Prevent users from creating their own IDs/Names in order to maintain consistency using defined naming patterns (docs)

Release 21.10, October 2021

  • Customize the aliquot naming pattern. (docs)
  • Record the physical location of freezers you manage, making it easier to find samples across distributed sites. (docs)
  • Manage all samples and aliquots created from a source more easily. (docs)
  • Comments on workflow job tasks can be formatted in markdown and multithreaded. (docs)
  • Redesigned job tasks page. (docs)

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!

The symbol indicates a feature available in the Professional Edition of Sample Manager or with a Premium Edition of LabKey Server.

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.

Sample Finder

Click Go to Sample Finder in the center of the dashboard to search for samples by properties of their parents and sources. Learn more in this topic:

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:

The next menu lets you control subcategories for the insights you are viewing.

  • Sample Count by Status offers:
    • All Statuses
    • With a Status
    • No Status
  • Sample Count by Sample Type -or- Assay run Count by Assay offer 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 these submenu options.

Learn more about samples in this section:

Freezer List

The freezer list presents a quick summary of your freezers, showing details, available capacity, and a color-coded bar indicating the types of samples in each freezer.

  • Hover over the Legend to see which colors are associated with which sample types.
  • Hover over any bar segment for details about what it represents, and click to jump to the storage view of those samples in that freezer.
Learn more about options available from the freezer list in this topic:

Main Menu

Throughout the application, you can access a master menu providing quick links to everything in the system.

Notebooks (Premium Feature)

Collaborate and record your work in data-connected Electronic Lab Notebooks. Use templates to create many similar notebooks, and manage individual notebooks through a review and signing process. Available in the Professional Edition of Sample Manager.

Learn more in this section:

Jobs List (Premium Feature)

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:

Related Topics

User Accounts, Groups, and Roles

This topic covers management of user access in LabKey Sample Manager. Administrators can perform these actions via the Administration option on the user menu.

Related Topics:

Add Users

To add one or more new users, an administrator first selects Administration from the user menu, then clicks Users, then Create.

In the popup:

  • Enter one or more email addresses, each on its own line for each user you want to create.
  • Select the desired Roles for the users you are creating:
    • You can assign multiple roles at once. Delete a role by clicking the 'X' for the item.
    • Learn more about the available roles here: Permission Roles
    • Note that all users added at once are assigned the set of roles you select. You can change these role assignments later.
  • Optional Message: You can add an optional additional message to include in the invitation email to your new users.
  • Click Create Users.
You will see the new user(s) added to the grid.

The new user will receive an email with a link to set a password and log in. If the new user should lose their initial invitation email, an admin can trigger the sending of another by selecting the row for that user and clicking Reset Password in the user details. See below.

Manage Users

To manage users, an administrator selects Administration from the user menu, then clicks Users.

You will see a grid of the active users already present in your Sample Manager project. You can use search, sort, and filter options on this user grid.

View User Details

To view the details for any user in the grid, check the box for that user. Details including effective roles are shown in a panel to the right.

From this panel, an administrator can click the buttons at the bottom to perform these actions on this individual user.

  • Reset Password: Send this user an email with a link to set a new password in order to access the site.
  • Deactivate
  • Delete
Click the user's Display Name in the grid to see even more details for that user.

Deactivate Users

Deactivated users may no longer log in, but their display name and group membership information will be retained for display and audit purposes. If the user is reactivated at a later time, this information will be restored. Deactivation is the recommended action for former employees, for example.

To deactivate a user, an administrator has two options:

  1. Check the box to select a single user you want to deactivate. Click Deactivate in the User Details panel on the right.
  2. You may also select one or more users simultaneously using the checkboxes in the grid, then select Manage > Deactivate Users.
For either option, you will be asked to confirm that this is the action you want to take by clicking Yes, Deactivate in a popup.

Note that if you are using Sample Manager with a Premium Edition of LabKey Server, you may want to remove this user's access to the Sample Manager project by revoking all permission roles, instead of deactivating them completely from the system.

Delete Users

Deletion of a user is permanent and cannot be undone; it is generally not recommended. A deleted user's display name will no longer be shown with any assignments or actions taken by that user. A deleted user cannot be reactivated to restore any information.

Instead of deleting, deactivation is recommended for any user who has performed any work in the system in the past.

One scenario in which deletion might be appropriate is if you originally create a new user with an incorrect email address or other error.

To delete a user, an administrator has the same two options as for deactivation:

  1. Check the box to select a single user you want to delete. Click Delete in the User Details panel on the right.
  2. You may also select one or more users simultaneously using the checkboxes in the grid, then select Manage > Delete Users.
You will be warned that deletion is permanent and need to click Yes, Permanently Delete to proceed.

View Inactive Users

Notice that the grid reads Active Users by default. To view the grid of deactivated users instead, select Manage > View Inactive Users.

You can check a box to see details for inactivated users, and buttons are offered to Reactivate and Delete a single user.

On the grid of interactive users, the Manage menu actions are also slightly different. You can select one or more rows to reactivate or permanently delete users. You can also switch back to the grid of active users.

Use Manage > View All Users from either view to see the combination of active and inactive users.

User Limit Alerts

When the number of active users approaches the application limit, administrators will see a warning message on the Administration > Users page.

Users of Premium Editions of LabKey Server can learn more 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:

Permission Roles

This topic is under construction for the 22.11 (November 2022) release of Sample Manager. For the previous version of this documentation, click here.

LabKey uses a role-based permissions model. This topic covers the permission roles available in Sample Manager and the process for assigning them to the appropriate users and groups.

Available Roles

Once users and groups have been defined, an administrator can assign them one (or more) of the available permission roles:

  • Editors: May add, edit, and delete data related to samples, assays, and jobs, but not storage information.
  • Editor without Delete: May add and edit, but not delete, data related to samples, assays, and jobs. May not edit storage information.
  • Readers: Have a read-only view of the application.
  • Administrators: Have full control over the application, with the exception of the storage related roles. This includes user management, permission assignments, and creating and editing sample types, assays, and job templates.
    • When Sample Manager is used with a Premium Edition of LabKey Server, there are two levels: Project Administrators and Folder Administrators. Learn more in the core LabKey Server documentation.
  • Storage Editors: Storage Editors may read, add, edit, and delete data related to items in storage, picklists, and jobs.
  • Storage Designers: Storage Designers may read, add, edit, and delete data related to storage locations.
  • Workflow Editor: This role allows users to be able to add, update, and delete picklists and workflow jobs. It does not include general "Reader" access, or the ability to add or edit job templates or any sample, source, or assay data.

Assign Roles to Users and Groups

Open user management by selecting Administration from the user avatar menu. Click the Permissions tab.

To add a user or group to any role:

  • First click the role section. You'll see the current members of that role.
  • Click the Add member or group dropdown and start typing a user's email address or the name of a user group.
    • Click the user email or group name to add to the role.
    • Selected users and groups will be shown in the panel for the role as you go.
    • Each time you select a user, the details for that user will be shown on the right to assist you.
  • In the image below, the Editor role is being granted to users named "team lead" and "lab technician"; the Reader role is being granted to the "reviewer".

Click Save.

Assign Administrator Role

Administrators have full control over the application, with the exception of the two storage-specific roles that must be separately granted. Admins can perform user management, permission assignments, and create and edit sample types, assays, and job templates.

Note that administrator permissions work differently when Sample Manager is used with a premium edition of LabKey Server. They are assigned on the same Permissions tab as other roles. Learn more in this topic:

The first user login created on the Sample Manager application is always an administrator. To assign the administrator role to other users or groups, any administrator can choose Administration from the user menu, then click the Settings tab.

Click the Application Administrators role panel and use the Add member or group... dropdown to select to whom to assign the administrator role. Type ahead to narrow the dropdown menu list.

Remove Users and Groups from Roles

To remove a level of access for a given user or group, reopen the interface for granting that role and click the X for the user or group you want to delete from the role. Removing a user from a role does not deactivate or remove the user account itself.

A note about role-based permissions: Users can be assigned multiple roles in the system, either independently or via groups, and each is independent. If a user is both Editor and Reader, removing them from the Reader role will not in fact remove that user's ability to read information in the system, because they will still have that access via the Editor role.

Related Topics

Manage Groups

Managing user accounts by groups can make it more efficient to assign permissions, workflow tasks, and review of notebooks. In many organizations, the specific person assigned to complete a task is not known in advance, but work can be picked up by anyone on a given team.

User Groups

To access the group management page, select Administration from the user menu, then click the Groups tab. All existing project level groups will be shown.

Create Group

To create a new group, type the name of the group and click Create Group.

You'll now see a new tile for your group. You'll also see a blue banner reading "You have unsaved changes" any time you edit groups. Click Save to save them.

Add Users to Groups

Expand the group by clicking anywhere in the tile and use the Add member dropdown to add members. You can add individual users, or other groups, to a group. Each time you add a new member, you'll see User Details on the right.

Click Save to update groups and assignments.

The "Users" Group

Note that there is always a "Users" group predefined in every project, sometimes used to represent every user with any access to the project, though this is not automatic. Users or groups must be explicitly added to this project group. For example, you might add all the groups you define to this group in order to assign "Reader" permissions and ensure a minimal level of read access to every group member.

You can also choose to delete this group (when it is empty) if you don't want to use it.

Delete Group

To delete a group, you must first delete the members by clicking the X for each, then click Delete Empty Group.

Related Topics

Manage Notifications

In-app Notifications

Notifications of interest to each user are shown in a menu in the header bar. If any background imports are in progress, the bell will be replaced with a . The number of waiting notices will be shown in orange, superimposed on the bell or spinner icon.

Click for a listing. Each notification has a corresponding status, time of completion, and link to either the successfully imported data, or to more information about an error.

Email Notifications

Users of the Professional Edition of Sample Manager can control whether they receive email for either Notebooks or Workflow or both. Email notifications allow users to learn about important events without having to manually check for them.

  • Notebook notifications are sent when notebooks the user is a part of are submitted, approved, or have changes requested.
  • Workflow notifications are sent about events that occur regarding jobs or tasks assigned to the user or which they are following.
For example, some events that trigger Workflow email notifications are:
  • A task assigned to me is ready to be completed
  • A job that includes tasks assigned to me is initiated
  • A job that I owned and completed was reactivated by another user
  • A comment was added to a task assigned to me

Receive Email Notifications

By default, all users will receive email notifications about Workflow and Notebook events that occur that they are part of, or are following. Users can choose to opt out of all email notifications by disabling these settings.

Select Settings from the user menu, then check the box for the Notifications you want. Uncheck the box to disable receiving email notifications.

Related Topics

Apply Naming Prefix

You can apply a naming prefix that will be added to all Sample and Source naming patterns to assist integration of data from multiple locations by maintaining a clear association with the original source of that data.

Apply Naming Prefix

This prefix is typically short, must be unique site-wide, and should be recognizable to your users. Before setting one, make sure you understand what will happen to the naming patterns and names of existing entities in your project.

  • All Naming Patterns for Sample Types and Source Types will be updated to include the new prefix.
  • New samples and sources created after the addition of the prefix will have names that include the prefix.
  • Existing samples and sources created prior to the addition of the prefix will not be renamed and thus will not have the prefix (or might have a different previously-applied prefix).
  • Sample aliquots are typically created and named including the name of the sample they are aliquoted from. This could mean that after the prefix is applied, new aliquots may or may not include the prefix, depending on whether the originating sample was created before or after the prefix was applied. Learn more about aliquot naming here: Aliquot Naming.
To set a prefix:
  • Select Administration from the user avatar menu.
  • Click the Settings tab.
  • Scroll down to the ID/Name Settings section.
  • Enter the prefix to use. You will see a preview of what a naming expression with the prefix applied might look like using a representative pattern, Blood-${GenId}, as an example.
  • Click Apply Prefix to apply it.
  • This action will change the Naming Pattern for all new and existing Sample Types and Source Types. No existing IDs/Names will be affected. Are you sure you want to apply the prefix?
  • Click Yes, Save and Apply Prefix to continue.

Force Usage of Naming Patterns for Consistency

To maintain consistent naming, particularly when using container-specific naming prefixes, you may want to restrict users from entering their own names for samples and sources. This requires that all types have a naming pattern that can be used to generate unique names for them.

When users are not permitted to create their own IDs/Names, the ID/Name field will be hidden during creation and update of rows, and when accessing the design of a new or existing Sample Type or Source Type.


  • Attempting to import new data will fail if an ID/Name is encountered.
  • Attempting to update existing rows during file import will also fail if an unrecognized/new ID/Name is encountered.
To disallow User-defined IDs/Names:
  • Select Administration from the user avatar menu.
  • Click the Settings tab.
  • Scroll down to ID/Name Settings.
  • Uncheck the box Allow users to create/import their own IDs/Names.
    • Note that to complete this change, all entities in the system must have a valid naming pattern. You will see a warning if any need to be added.

Related Topics

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 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 cloud-based 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 Sample Manager?

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, you can create your own field (either text or integer) to hold your own barcode values. Or, with the addition of a "UniqueID" column, Sample Manager will generate unique barcodes for samples for you. 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 includes a robust and flexible freezer management solution. Design virtual storage to match your physical storage. Easily find samples, or empty space for storing new samples. Track volume and check-in and check-out to support your workflow. Control access with specific storage roles. 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.

Use custom templates to make it easier to format your data.

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. You can also use controlled vocabularies for text fields, 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. Multi-tabbed sample lists can be exported as multi-tabbed Excel spreadsheets.

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, Professional Edition users have the option to let the application infer fields in the data structure from the columns in a spreadsheet.

Are the Assays customizable? Can I create my own assays? (Professional Edition Feature)

Absolutely, with the Professional Edition of Sample Manager. 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.

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.

Jobs, Tasks, and Templates (Professional Edition Feature)

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 the Professional Edition of 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 Professional Edition of Sample Manager, 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 Sample Manager export their 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. One option is to use a controlled vocabulary text field to track information and let users select from lists instead of free entering values.

Related Topics

More Questions?

Have more questions or need additional information? Please get in touch with us: