2. Projects

Projects are the primary organizational unit within Mosaic. Typically, a project will represent an individual case, which could be a single patient, a family (for example, a family trio consisting of a proband and parents), or any other desired group. The projects page consists of the following pages:

2.1. Project Home

The Project Home acts as a dashboard for the project where important information can be aggregated. If the project is included in any collections, they will be listed at the top of the page. Which collections a project is in can be managed by clicking the +/- icon here.

The Recent Documents card at the top of the page provides quick links to project documents, e.g. pdf files. This makes it easy to view documents like clinical reports for a case.

Important attributes, conversations, charts, or variants can be pinned to the Project Home to provide a curated set of information immediately available upon entering the project. How to pin these objects is covered in the documentation sections dedicated to them.

2.2. Samples

Projects samples refer to people, typically a proband or family member. The Samples page (also present in collections) provides a list of all of the samples in the project along with any selected sample attributes associated with the sample. Important sample attributes to populate include Relation which defines how the sample is related to the proband; Affected Status describing whether the sample is affected or not; and the Sex of the sample. As with other tables, the displayed columns can be edited by clicking the Edit Columns button at the top right of the table.

Check boxes to the left of each sample allow individual or groups of samples to be selected and then the Actions button provides a number of options, or the Launch App button allows different web apps to be launched

2.3. Project Attributes

Project Attributes displays all of the project-level (as opposed to sample-level) attributes associated with a project. From here, we can create new (this is discouraged in most projects - attributes should be created in projects or templates dedicated to holding attributes), import, edit attribute values, or pin them to Project Home. Project attributes are discussed at length here

2.4. HPO Terms

2.5. Variants

2.6. Conversations

2.7. Documents

2.8. Analytics

2.9. Analyses

2.10. Settings & More

A lot of project information is stored in the Projects Settings. These are all addressed here

2.10.1. Settings

Project Information The project information section allows basic information about the project to be edited. This includes the name, nickname, description etc, but also the privacy level of the project

Project Members This section of the settings lets you look at who has access to the project, what their roles are as well as invite or edir peoples roles. Exactly what you are allowed to do here depends on your own role in the project. Only people with Admin access or above can modify users of a project. The top of this section shows a table of all current members and their roles (Figure 2.1). To edit a users role (if you have permission), select the role dropdown next to the users name and change their role

Figure 2.1. Review users with permission to access a project

To grant access to the project for new users, scroll down to the Invite a Collaborator table and search for the user name. Only users with active Mosaic accounts can be added. When the user has been selected, choose a role and add the user to the project. Typically users are added as Members. If the new user should be authorised to grant project access to other users, they can be given the Admin role.

Figure 2.2. Add a user to a project

Project Tasks

Project Templates

2.10.2. Data Files

2.10.3. Applications

2.10.4. Genes

For information on genes, see the dedicated section in the docs