Opening Sequence Miner¶
Sequence Miner is a research tool for integrated analysis of genotype and phenotype data on patients. Clinical and other phenotype data can be imported into Sequence Miner through the metadata query language NOR (Non-Ordered Relational). Data fields can be sorted and filtered allowing the user to quickly classify patients into categories (e.g., affected and unaffected) The NOR-defined subsets can then be used as input list(s) for genomic analysis applications in Sequence Miner called report builders that apply the GOR (Genomically Ordered Relational) query language.
Sequence Miner can be opened from CSA in several different ways. You must be logged in to CSA in order to use Sequence Miner.
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. If that option is presented, select Clinical to continue.
Select the Clinical option to continue¶
If your user account has multiple projects associated with it, you will be asked to select the project you wish to work with. Select a project by clicking on the project name.
The project selection screen¶
From the CSA dashboard¶
To open Sequence Miner from the CSA dashboard, click the Sequence Miner link under Research Analysis.
In the dialog that opens, click Allow to launch Sequence Miner.
This opens the Sequence Miner front page in a new window, which displays the Reports tab, File Explorer, and toolbar.
From the Study overview¶
To open a specific study for analysis in Sequence Miner, click the Sequence Miner link on the Study Overview page of the selected study.
This opens the Sequence Miner view of the selected study only.
From the Advanced report¶
Clicking the Advanced report link in the Study Overview opens a new page that displays all variants in the project, organized into tabs and subsections. If you are loading the advanced report for the first time, this page may take a couple of minutes to load.
When the data has finished loading, you can open Sequence Miner from three places on this page:
To open the query that generated the displayed data in the Sequence Miner query window, click Open query in Sequence Miner at the top right-hand side of the page.
To open a variant of interest in the Sequence Miner Genome Browser, click on the variant coordinates from any view of the variant listing.
The Genome Browser opens at the exact location of the selected variant coordinates.
To open a gene of interest in the Sequence Miner Genome Browser, click on the gene name in any view of the variant listing and select Open in Sequence Miner.
The Genome Browser opens at the exact location of the selected gene.
Installing Sequence Miner from CSA¶
If you have not previously installed Sequence Miner before trying to open it from CSA, you will be prompted to download the Sequence Miner launcher application. Note that Sequence Miner is always run from within CSA, but it is necessary to install the launcher application before using Sequence Miner.
To download and install Sequence Miner, click Install Sequence Miner. The system will detect your computer’s operating system and begin downloading the appropriate version of the Sequence Miner application.
The installer file is called NextCode_installer_osx.dmg on a Mac and NextCode_installer_win.exe on a PC. It will be downloaded to the Downloads folder in your home directory. Find the file in your Downloads folder and double-click it to continue.
Note
Sequence Miner is a Java program. The publisher of Sequence Miner may appear as “DeCode Genetics ehf” or “NextCODE Health”.
Mac-specific instructions¶
On a Mac, the operating system will verify the installer file and open a Finder window with the package to be installed.
Double-click the package to start the installation¶
Double-click the package to start the installation and follow the Setup instructions.
Click Next to finish the installation¶
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 CSA.
Return to CSA and click Open Sequence Miner to open the Sequence Miner application. Sequence Miner opens with the Reports tab preloaded.
Return to CSA to open the application¶
For information about Sequence Miner report builders, refer to the Sequence Miner User Guide.
PC-specific instructions¶
If you are using a PC running Windows, your operating system may not allow automatic installation of the Sequence Miner launcher application. In the Windows Defender SmartScreen, click the More info link and then click Run anyway to run the launcher application.
Windows Defender SmartScreen prevents the unrecognized app from starting¶
Continue to install the program as you would normally. If you are unable to do this (due to the restrictions on your access), please contact your system administrator for help.
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 CSA.
Return to CSA and click Open Sequence Miner to open the Sequence Miner application. Sequence Miner opens with the Reports tab preloaded.
Return to CSA to open the application¶
For information about Sequence Miner, refer to the Sequence Miner User Guide.
Troubleshooting the installation¶
Older versions of Sequence Miner¶
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 unistall the launcher application and reinstall (see Installing Sequence Miner from CSA).
To unistall the Sequence Miner launcher on a Mac, open a Finder window and browse to the Applications folder. Select the SequenceMinerLauncher application and move it to the Trash.
Unidentified developer¶
Some computers will report that the Sequence Miner launcher is from an unidentified developer. This is a known Java issue, and you should run the downloaded file.