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Getting around the platform

Top navigation panel

The Top navigation panel of the platform serves as a guide to the platform. It contains:

Dashboard, Cases and Add new case buttons lead to the corresponding pages
Case search bar
Settings dropdown menu activated by clicking on the user name or profile picture
Help dropdown menu activated by clicking on the question mark icon
Emedgene Applications menu activated by clicking on the app launcher icon on the left

As of version 2.26:

Emedgene Applications menu

The Emedgene platform is divided into two applications:

Analyze - genomic analysis workbench,
Curate - the knowledge management system.

To switch from Analyze to Curate:

Go to the nine-dot app launcher icon located on the left of the Top navigation panel and select Curate from the dropdown menu.

To switch from Curate to Analyze:

Go to the nine-dot app launcher icon located on the Curate navigation panel and select Analyze from the dropdown menu.

Dashboard

The Dashboard provides a glance at key performance indicators for an organization and depicts an overview of the user activity on the Emedgene platform.

This page is divided into two panels and contains the following subsections:

Lefthand panel

Emedgene Knowledge Base panel reveals the total amount of known polymorphisms, pathogenic variants, and gene-disease connections considered during analysis. It also indicates the number of scholarly publications processed by Emedgene's novel textual recognition platform, backed by natural-language processing and artificial intelligence.
Diagnostic Yield panel presents the proportion of "solved" cases out of the total number of the organization's cases of the same type.
Status Diagram panel displays the total number of the organization's submitted cases as well as the numbers of cases under each status.
Stale Cases panel highlights the cases that are stuck at one of the intermediate stages of the analysis, and are not finalized.

Righthand panel

Network Activities: The right panel displays a timeline of activities performed by multiple users within the organization. This log includes activity like creating a case, verifying a Preset, changing a Case status, generating a report, etc.

Settings

Click on the user initials or profile picture at the rightmost corner of the Top navigation panel to open the Settings dropdown menu. From there, you can enter:

My Settings

Add or edit your professional credentials, profile picture, contact information and organization's details, and review roles and permissions granted to you.

Management

Manage data storage, custom Case statuses, Case labels, create, edit and delete gene lists, set how long until a case becomes "stale", and assign user groups.

Note: Organization settings are accessible only for users having a Manager role.

User Management

Add, activate and inactivate users and manage user roles.

Network

Create networks, establish data sharing policies for each network, delete and leave networks.

Organization Settings (33.0+)

Choose a software version for your organization, set up a case identifier, and select your preferred URLs (the latter - only for ILMN cloud users).

Help

Next to the user's initials or profile picture is a question mark Help icon. Clicking on this icon expands a dropdown menu with the following options:

Support Chat: reach out to our Customer Support team anytime without leaving the page;
What's New: check out the new features, enhancements, or any other updates related to the platform.

Caution: Please be aware that when performing a task, such as uploading a new sample, clicking on the buttons in the Top navigation panel may terminate the progress. However, for the most part, changes and annotations made on the analysis pages are auto-saved.

User roles

Emedgene users are defined by roles. Roles are managed in Settings > User Management. Access to the User Management tab is restricted to those with the appropriate permission.

The available roles for Emedgene are described below:

User Role

Description

Component / Flow

User Level

If you are not seeing part of the roles from the user management interface, please be in touch with our support.

Help

Click on the question mark icon of the Top navigation panel to open the Help dropdown menu.

From there, you can access:

Help Center. Feeling curious? Dive right in.
What's New. Check out the release notes to be on top of our latest and greatest features!

Okta identity management

The Emedgene platform utilizes the Okta Identity Management solution to control user access. This improves user management, enhances access and authentication security, and allows organizations to implement single sign-on for their users.