All pages
Powered by GitBook
1 of 8

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:

  • Help Center: Access the user manual and learn how to leverage NextUser rolespowerful features to serve your patients or advance your research;

  • What's New: check out the new features, enhancements, or any other updates related to the platform.

  • Coming soon: Walkthroughs & Feature Requests

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. In Illumina environments only, Roles and Permissions are now managed through IAM (previously via User Management in EMG Settings) . Access to the User Management tab (Users card) is disabled and redirects to the IAM application.

The available roles for Emedgene in IAM are described below:

Emedgene Role/IAM Scope
Description

Acmg Tags

Allow user to see ACMG Tags

Acmg Tags Edit

Allow user to edit ACMG classification

Add New Test

Allow user to add new test

Apidocs

Allow user to see api docs

Auto Analysis

Allow seeing auto analysis results

Candidate Compound With

Allow user to merge and split compound variants

Change Finalized Test Status

Allow user the user to unlock a finalized case

Check Preset

Allow user to mark case's presets as reviewed

Comment

Allow user to activity comment

Comment Delete

Allow user to delete comment

Create Custom Preset Group

Allow user to create Custom Preset Group

Create Report

Allow user to create report template

Create Variant

Allow user to create variant manually

Detailed Version

Allow user to see all services versions

Developer

Allow user to see developer settings

Download

Allow user to download files

Due Date

Allow user to edit due date

Edit Case Labels

Allow edit labels of a case

Edit Test

Allow user to edit test's info

Evidence

Allow seeing evidence page

Evidence Edit

Allow user to edit the evidence page

Evidence Generate

Allow user to generate intial evidence

Evidence Pathogenicity Edit

Allow user to edit evidence pathogenicity

Evidence Text Edit

Allow user to edit evidence text

Gene Lists Read Only

Allow user to show the gene lists

Gnomad Genome

Allow user to see GnomAD Genome

Kms

Allow user to view Curate

Kms Create Gene

Allow user to create a new gene in Curate

Kms Create Variant

Allow user to create new variant in Curate

Kms Delete Variant

Allow user to delete a variant from Curate

Kms Export

Allow user to export/update variants from Analyze to Curate

Kms Export Data

Allow user to export genes and variants data from Curate

Kms Import Network Variant

Allow user to import from network variants from Curate

Kms Update Acmg

Allow user to update variant ACMG tags in Curate

Kms Update Disease Id

Allow user to update variant disease ID in Curate

Kms Update Gene Interpretation

Allow user to update gene interpretation in Curate

Kms Update Gene Note

Allow user to update gene notes in Curate

Kms Update Gene Transcript Ref Sequence

Allow user to update a gene selected transcript in Curate

Kms Update Interpretation

Allow user to update variant interpretation in Curate

Kms Update Note

Allow user to update variant note in Curate

Kms Update Pathogenicity

Allow user to update variant pathogenicity in Curate

Kms Update Transcript

Allow user to update variant transcript in Curate

Load Bam Igv

Allow user to load BAM files to desktop IGV

Manage Auto Analysis Tier

Allow user to update AI Shortlist mode from Org settings page

Manage Case Default Page

Allow user to manage default Case page

Manage Case Identifier

Allow user to manage case identifier

Manage Case Participants

Allow user to add or remove case participants

Manage Column Order

Allow user to manage analysis column order setting

Manage Empty Trash

Allow user to empty cases from trash bin

Manage Gene List Visibility

Allow user to manage gene list visibility

Manage Gene Lists

Allow user to manage gene lists

Manage Kit Bed

Allow user to manage kits and bed uploads

Manage Labels

Allow user to manage labels

Manage Multiple Tags

Allow user to enable multiple tagging

Manage Organization Dbs

Allow user to manage organization databases

Manage Platform Version

Allow user to manage platform version

Manage Poc

Allow user to update POC from Org settings page

Manage Pon

Allow user to add or delete PONs

Manage Pipeline Versions

Allow user to update pipeline version from Org settings page

Manage Quality Parameters

Allow user to manage sample quality configurations

Manage Report Timestamp

Allow user to manage report timestamp

Manage S3 Credentials

Allow user to manage organization's s3 credentials

Manage Sv Annotation

Allow user to manage SV annotation thresholds

Manage Test Presets

Allow user to create presets from gene lists

Manage Url Pattern

Allow user to manage organization URL pattern

Manager

Organizational admin (manager) role

Manager Edit Variant Tags

Allow user to manage variants tag

Manager Support Access

Enable/disable support access in management

Network

Allow user to see available networks, request to join, etc.

Network Create

Allow user to creare new network

Network Manage

Allow user to manage network

Pheno Score Col

Allow user to see the Phenomatch score in the Analysis table

Phenomatcher

Allow user to filter by phenotipic match

Preset Create

Allow user to create presets from analyze and settings page

Preset Delete

Allow user to delete a preset from the list of available Filterset in a preset group

Preset Group Create

Allow user to create and edit a preset groups

Preset Group Default

Allow user to assign a default preset group

Preset Group Download

Allow user to download a legacy preset group JSON file

Preset Group Hide

Allow user to hide a preset group

Preset Group Revert

Allow user to revert a migrated preset group

Preset Group Upload

Allow user to upload a JSON file to the create new preset group

Preset Lock

Allow user to lock and unlock of a preset

Preset Manage

Allow user to view/edit a preset in JSON format

Re Analysis Filter

Allow user to see re analysis candidates

Re Upload Tab

Allow user to re-upload files

Render Template

Allow user to preview a report template

Report

Allow user to export a report

Report Preview

Allow user to preview report as draft

Sanger Edit

Allow user to edit Sanger

Storage Provider

Allow user to manage storage providers

Tag Variant

Allow user to tag a variant

Test Status

Allow user to change a test status

Test Status Move To Trash

Allow user to change test status to move to trash

Test Status To Finalized

Allow user to change case status to finalized

Transcript Edit

Allow user to change the default transcript for variants

Unknown Phenomatch

Allow user to use unknown phenomatch variant filter

Upload

Allow user to upload samples

User

Regular user role

User Management

Allow user to manage users

User Read

Allow user access to organization data

User Rerun Case

Allow user to re-run cases

Versions Tab

Allow user to access the Versions tab

If you are not seeing some of the roles in IAM, please be in touch with tech 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.

​