Premium Feature — Available in the Professional Edition of Sample Manager and all Premium Editions of Biologics LIMS. Also available when Sample Manager is used with a Premium Edition of LabKey Server. Learn more or contact LabKey.
Projects allow users to organize and partition sensitive data into projects within the application, all while maintaining a shared storage environment. Data structures and resources like reagent lists can also be shared lab-wide to support consistency, while individual teams work with their own secured data.
In this video, you will see how to configure and use Projects to work with data across different teams using Sample Manager Professional.Note that there have been improvements to the interface and user experience for working in Projects since the making of the video.
Overview
Without the use of Project organization, Sample Manager does not partition data for different teams. Permissions are granted to all data simultaneously in a single "container".When you enable Projects in the Professional Edition of Sample Manager, data can be grouped and partitioned by teams.
Home Project and "Sub" Projects
The home project is at the top level and provides shared definitions and storage configurations. Data can be added directly in the home project or to the individual "sub" projects as appropriate. Permissions are controlled independently in each project, making it easy to partition separate team spaces.
Sample Types, Source Types, etc. are defined in the home project to support lab-wide consistency. Administrators can create and/or edit these structures from within subprojects, but the changes will be made to the home project definition and shared by all subprojects.
Storage systems like freezers are also defined in the home project to match the shared physical space. Individual teams can see the details of stored samples they have permission to read, but only see space allocated to other teams as "occupied".
Reports and views of all data you have access to can be created in the home project, summarizing all the data an individual user has access to.
Create shared resources like reagents in the home project so that they can be shared & viewed by all projects.
Use project permissions to partition each study from one another making it easy to operate in compliance with regulations.
Note: If you are familiar with the way that the terms "projects" and "folders" are used in LabKey Server, the top level Sample Manager "Home Project" or "application" level is equivalent to a LabKey project. A Sample Manager Project (sometimes called a subproject) is equivalent to a LabKey folder within that LabKey project.
Manage Projects
To manage Sample Manager Projects, open the application and select > Projects.On the Projects administration page, you'll see a listing of any existing projects, with the first selected by default. You can edit existing project details or create a new one.
Create New Project
Click Create to add a new project. Enter the Project Name and uncheck the checkbox if you wish to provide a different label.For the panels below the project name, uncheck boxes if you want to limit the resources that are shown in your new project. The default is that everything from the home project is visible in all projects. Learn more about each section below.
When first created, only administrators can view a new project. This can be useful when configuring the project for a team to ensure the users only access it when ready.You can configure project permissions immediately when you create it by clicking Update project permissions. Later you can also reach this page by clicking the for the project on the main menu, or from anywhere in the project by selecting > Permissions.Note that within a sub-project, the Application Administrator role is not assignable; it can only be set at the top application level. On a Premium Edition of LabKey Server, you can set the Folder Administrator role to apply to this project only, but cannot set the application-wide role.Learn about configuring permissions in this topic:
Click it's name from the Projects dashboard (select > Projects).
Click Delete Project.
When a project is deleted, all data contained in it will also be deleted. The administrator will see a warning detailing the project's contents and need to confirm to proceed.
Select Data in Project
An administrator can restrict the Source Types, Sample Types, and Assay Designs that are visible in a given project. This can be configured during project creation or later by editing project settings.You'll see all the Source Types, Sample Types, and Assay Designs available in the home project. By default, everything available will be visible in the project, but you can uncheck boxes for types of data that will not be used in the project. If data is present, you'll see a message about what will no longer be visible.Note that 'hiding' or deselecting a data structure here does not delete any data that may exist using it. It just simplifies dropdown menus for users. The hidden entities will not be seen, but will still be present (and lineage relationships preserved). Nor does hiding a type of data prevent it from being used in the future if these settings are edited.The projects in which a given data structure is visible can also be set while creating or editing the data structure itself in the Projects panel. For example, if the "Labs" Source is not in use for "Project B", the Projects panel might look like this:
Exclude Sample Types from Dashboard Insights
When using Projects in Sample Manager, the ability to exclude Sample Types from Dashboard Insights is moved to the Projects tab. There is a Dashboard section for each project, including for the top level application, or home project.Learn more in this topic:
An administrator can limit the storage systems that are accessible from a given project by using checkboxes in the Project Storage panel. For example, if you wanted to create a project for a team that would only work with a single freezer in their local lab, you could hide all other storage systems.Note that this does not delete any storage or change how samples are stored in the hidden freezers, it just simplifies the dropdown menus for users in the project.The projects in which a given storage system is visible can also be set while creating or editing the storage definition using the Projects panel below the hierarchy. For example, if this freezer is not in use in Project Beta, that box can be unchecked:
Work within Projects
Once one or more projects have been defined, the main menu will include the name of the current project and a panel on the left for selecting the home project or one of the "subprojects". Each user will see only the projects to which they have access.To navigate, click the name of the desired project, then the page of interest from the main menu. When you hover over a project name, you'll see quick links to key pages for that project:
Dashboard
Administration
When you are in the home project, you can add or manage data and definitions like Sample Types and Assay Designs for all the projects to be able to share.When in a project, you will still see data for all projects you can access, but additional data added will only be available in that project and visible only to users permitted to see that project's contents.Note that changes like editing a Sample Type definition in a project require permission to make those changes at the home project level and they will apply to all projects.Learn about actions across projects in this topic:
All users must have Read access to the top level project.
Recommended: Only assign non-admin users Read access (and Storage Designer/Editor as appropriate) in the top level Home project. Edit/add permissions will be granted in individual projects.
The Home project is where all Source Types, Sample Types, Assays, Storage Systems and Templates for ELN and Workflow are defined.
Administrators can create and edit Source Types, Sample Types, Assays, Storage Systems from within sub projects, but all changes are made in the home project definitions and apply to all subprojects.
Add all "shared resources" in the home project that you want to be able to access in other projects, such as shared reagent lists, etc.
Sub Projects
Project/Study/Team-based access to sources, samples, assay data, workflow & ELNs.
Within a sub project, users can edit/update their project data.
From the home project, users can read their project data (and all data they can access).
For data to be readable by everyone but that does not need to integrate (or inherit from) other data, create a project that everyone has access to.
On the Projects administration page, you'll see a listing of any existing projects, with the first selected by default. You can edit existing project details or create a new one.
For the panels below the project name, uncheck boxes if you want to limit the resources that are shown in your new project. The default is that everything from the home project is visible in all projects. Learn more about each section below.
Note that within a sub-project, the Application Administrator role is not assignable; it can only be set at the top application level. On a Premium Edition of LabKey Server, you can set the Folder Administrator role to apply to this project only, but cannot set the application-wide role.Learn about configuring permissions in this topic:
When a project is deleted, all data contained in it will also be deleted. The administrator will see a warning detailing the project's contents and need to confirm to proceed.
Note that 'hiding' or deselecting a data structure here does not delete any data that may exist using it. It just simplifies dropdown menus for users. The hidden entities will not be seen, but will still be present (and lineage relationships preserved). Nor does hiding a type of data prevent it from being used in the future if these settings are edited.The projects in which a given data structure is visible can also be set while creating or editing the data structure itself in the Projects panel. For example, if the "Labs" Source is not in use for "Project B", the Projects panel might look like this:
Learn more in this topic:
Note that this does not delete any storage or change how samples are stored in the hidden freezers, it just simplifies the dropdown menus for users in the project.The projects in which a given storage system is visible can also be set while creating or editing the storage definition using the Projects panel below the hierarchy. For example, if this freezer is not in use in Project Beta, that box can be unchecked:
When you are in the home project, you can add or manage data and definitions like Sample Types and Assay Designs for all the projects to be able to share.When in a project, you will still see data for all projects you can access, but additional data added will only be available in that project and visible only to users permitted to see that project's contents.Note that changes like editing a Sample Type definition in a project require permission to make those changes at the home project level and they will apply to all projects.
Learn about actions across projects in this topic:
