Getting Started¶

Installing the Sequence Miner Launcher¶

Sequence Miner is launched from Clinical Sequence Analyzer (CSA), and you must be logged in to CSA to open Sequence Miner. If you are opening Sequence Miner for the first time (or have previously removed it), you will need to install the launcher first.

To install the Sequence Miner Launcher from CSA, log in to CSA and select a project (see also Opening Sequence Miner).

In the Project Overview, click the Sequence Miner link under Research Applications in the dashboard.

The launcher starts and detects whether Sequence Miner has been previously installed. This may take a few minutes. If Sequence Miner has not been previously installed, the installation dialog opens. Click Install Sequence Miner to download the iauncher.

_images/no_application_02.png — The launcher detects whether Sequence Miner has previously been installed¶

_images/sm_installation.png — Click Install Sequence Miner to download the launcher¶

The launcher file is called NextCode_installer_osx.dmg on Mac and NextCode_installer_win.exe on Windows, and is automatically downloaded to the Downloads folder in your home directory. Locate the file in your Downloads folder and double-click it to continue.

To finish the installation, follow the instructions below for Installing on Mac or Installing on Windows.

Once installed, the Sequence Miner Launcher automatically checks for updates every time you open Sequence Miner, so that you are always running the latest version (see also Viewing version information).

Installing on Mac¶

On Mac, the operating system verifies the installer file and opens a Finder window with the package to be installed.

Double-click the package to open the Setup Wizard. To complete the installation, follow the instructions in the wizard.

When the installation is complete, a program called SequenceMinerLauncher is added to the Applications folder on your computer.

Note

Do not open Sequence Miner from this application. Sequence Miner must be launched from within CSA.

Return to CSA and click Open Sequence Miner in the installation dialog.

In the confirmation dialog that opens, click Allow.

Sequence Miner opens with the Reports tab preloaded. To open Sequence Miner from other locations in CSA, see Opening Sequence Miner.

Installing on Windows¶

If you are running Windows, your operating system may not allow the Sequence Miner launcher to be automatically installed.

_images/win_fail.png — Windows Defender SmartScreen prevents the unrecognized app from starting¶

Then continue to install the program as normally. If you are unable to do this (due to the restrictions on your access), please contact your system administrator for help.

_images/setup_win_01.png — Continue the installation on Windows¶

When the installation is complete, a program called SequenceMinerLauncher is added to the Program Files folder on your computer.

Note

Do not open Sequence Miner from this application. Sequence Miner must be launched from the CSA website.

Return to CSA and click Open Sequence Miner in the installation dialog.

In the confirmation dialog that opens, click Allow.

Sequence Miner opens with the Reports tab preloaded. To open Sequence Miner from other locations in CSA, see Opening Sequence Miner.

Troubleshooting the installation¶

If you are running an older version of the Sequence Miner launcher application, you may be prompted with an alert stating that the signature for the downloaded application could not be verified. If that is the case, you should uninstall the launcher application and re-install as previously described (see Installing the Sequence Miner Launcher).

_images/security.png — If you see the error message above, you should reinstall the Sequence Miner launcher application¶

Uninstalling Sequence Miner¶

To uninstall Sequence Miner on Mac, open a Finder window and browse to the Applications folder. Select the application labeled SequenceMinerLauncher and throw it in the trash.

To uninstall Sequence Miner on Windows, open Local Disk > Program Files and locate the SequenceMinerLauncher folder. Open the folder and double-click the uninstaller to uninstall the launcher.

Opening Sequence Miner¶

To open Sequence Miner, first log in to CSA. Sequence Miner can be opened from several locations within CSA, including the Project overview, Study overview, and Advanced reports.

_images/login_01_login.png — Enter the email address you used to create your account¶

Depending on your system configuration, you may be asked to select where you would like to start. In that case, select Clinical to continue.

If your user account has multiple projects associated with it, select a project by clicking on the project name.

From the Project overview¶

When you have logged in to CSA and selected your project, you can open Sequence Miner from the Project overview by clicking the Sequence Miner link under Research Analysis in the dashboard.

From the Study overview¶

To open Sequence Miner from the study overview, select a study and click the Sequence Miner link in the menu bar on the Study Overview page.

_images/openSM-studyoverview.png — Open Sequence Miner from the study overview¶

From Advanced reports¶

Selecting Advanced report in the study overview opens the variant listing, which displays all variants in the project. From this view, you can open Sequence Miner from the following locations:

Click Open query in Sequence Miner at the top right-hand side of the page to open the query that generated the displayed data directly in the Sequence Miner query window.
Click the hyperlinked variant coordinates of an item in the variant listing to open the selected variant coordinates in the Sequence Miner Genome Browser, zoomed in to the exact position.

Opening Sequence Miner from the variant listing in the Advanced report¶
Click the hyperlinked gene name and select Open in Sequence Miner from the drop-down menu to open the selected gene in the Sequence Miner Genome Browser.

Open Sequence Miner from the hyperlinked gene name in the Advanced report¶

Viewing version information¶

To view details about which version of Sequence Miner you are running, open Sequence Miner and click the Info icon in the toolbar on the left-hand side.

In the About Sequence Miner pop-up, you can see the version information displayed.

Restoring a session¶

If your Sequence Miner session times out, a pop-up dialog prompts you to refresh the session. If the timeout occurs because of a lost internet connection, your session should restore automatically once the connection is regained.

File Explorer¶

The File Explorer in Sequence Miner allows you to access files on various storage platforms as well as on your local machine. It is not possible currently to move files between these storage platforms.

The File Explorer can be opened and closed by clicking the first icon in the toolbar on the left-hand side of the Sequence Miner window. When you open the File Explorer, a folder tree of the available files for your study, including any sample data associated with the study, is displayed along with your instance’s current version of the referenceData.