Tools

In this central location you can access and launch all tools maintained by the NIMH Data Archive. In all cases, a recent version of Java is required in order to use NDA tools. OpenJDK is not supported.

GUID Tool

Researchers throughout and beyond the field of mental health research use the NDA GUID Tool, originally developed for the use of the autism research community and the National Database for Autism Research (NDAR), to generate participant identifiers. The GUID Tool takes personally information provided by research participants and uses it to securely create a unique identifier. Using this tool, participant data can be linked across studies and laboratories while always maintaining the participant's privacy. In order to use this tool, you will need a user account with the appropriate permission assigned.

Launch the GUID Tool


Validation and Upload Tool

Contributors harmonizing and uploading their data to the NIMH Data Archive must use the Validation and Upload Tool to send their data and complete this process. This tool connects to the Data Dictionary, and then allows you to load data templates and validate them against their definitions. This helps ensure that data in NDA is harmonized to a standard and serves as a "pre-upload" QA check on your data. After data is successfully harmonized, the same tool is used to package and upload the data to your NDA Collection. In addition to working with CSV data templates, the tool also supports direct uploads from a hosted AWS-RDS database.

Launch the Validation and Upload Tool


Download Manager

Users approved for access to NDA shared data can use the Download Manager to view and download data packages they have added to their account or created using the query tools. Access to download data to non-AWS internet addresses is limited to 20 Terabytes over 30 days. For more detail, including examples, please read about our user download threshold.

Note: Data packages containing omics data must be accessed through the cloud and cannot be downloaded directly using this tool. In addition to the Download Manager tool described below, a python command line downloader is also available.

The Download Manager tool is provided as a Java Web Start application, which is launched using a Java Network Launch Protocol (JNLP) file downloaded from NDA. Opening the JNLP file requires the Java Runtime Environment (JRE) for Java 8 , which will download resources from NDA necessary to launch the application. Note only Java 8 is compatible with NDA Download Manager.

Prerequisites

To launch (i.e., run) the tool, the following prerequisites must be satisfied:

  • Installation of Java Runtime Environment (JRE) for Java 8
  • Copy of JNLP file, or URL for the JNLP file

Verify you have the 1.8 version of the JRE installed by opening a command prompt (Windows) or terminal window (Mac and Linux), then enter the following command: java -version and press the ‘Enter’ key. You should expect to see output displaying either the installed version of Java Runtime Environment (JRE) or an error message indicating that the command is not recognized. The JRE version should begin with 1.8.0_ followed by the specific update version (i.e., java version "1.8.0_261").

To obtain a copy of the JNLP file, click Download NDA Download Manager JNLP. The browser should begin downloading a file named DownloadManager.jnlp.

 

Installing Java SE Runtime Environment (JRE) for Java 8
 

If you were not able to successfully verify installation of JRE version 1.8, please download the installation file for your operating system and follow the instructions provided for installation. Note that other JRE versions are not compatible with this tool.

Windows: https://www.java.com/en/download/help/windows_manual_download.xml

Mac: https://www.java.com/en/download/help/mac_install.xml

Linux: https://www.java.com/en/download/help/linux_x64_install.xml

Further instructions for installing Linux JRE for Java 8 and switching between Java versions are provided here.

 

 

Launching the Download Manager

After successfully installing JRE 1.8, you should be able to double-click on the DownloadManager.jnlp file that was downloaded (see prerequisites). The installation should register the Java Web Launcher executable (javaws) when attempting to open or run a jnlp file. You may need to add an exception for the https://nda.nih.gov URL in the JRE configuration to allow the application to run.

If the system does not recognize which application to use for the jnlp file:

  1. Open a command prompt (Windows) or terminal (Mac and Linux),
  2. Change to the directory where you downloaded the DownloadManager.jnlp file, typically the Downloads folder for your user, and
  3. Enter the command: javaws DownloadManager.jnlp.

When the Java Web Launcher opens the DownloadManager.jnlp file, several files will be downloaded and a prompt will be displayed the text: Do you want to run this application?

The prompt will show the following information:

 

Name: Download Manager
Publisher: National Institutes of Health
Locations: https://nda.nih.gov Launched from downloaded JNLP file.

This application will run with unrestricted access which may put your computer and personal information at risk. Run this application only if you trust the locations and publisher above.

 

Click on the Run button to open the Download Manager, and you will be prompted to enter your NDA username and password. After entering a valid username and password, the tool will open.

Note: There may be some delay after entering your credentials, especially if your user has a large number of packages or packages include a large number of files.

A new screen will open with Warning describing the terms of use for the Download Manager. After clicking the Accept button the tool will open a screen with a table listing your packages.

Using the Download Manager

Select the location for where packages should be saved to by clicking the "Browse" button, and then selecting a directory with enough space for downloading your package. The size is provided in the table that displays each of your packages. The default location will be your user’s home directory.

Select the check box next to the package you wish to download and click the Start Downloads button. The package status must be 'Ready to Download' before you can begin downloading files. If the package status is Creating Package, press the Refresh Queue button to update the status. Depending on the size (number of subject records and files) of the package this can take up to 30 minutes after initiating the data package request in the NDA Web Application.

Download Manager will create a directory with the package name, in the location you selected. If any errors are encountered during the download, an errors.txt file will be created in this directory with detailed error messages, and the progress bar will not reach 100% completion.

Depending on your internet connection and performance of the storage device (internal hard drive, network attached storage, etc.) downloading an entire package may require several days to complete. Users can typically expect packages in excess of 1 Terabyte to take several days to download.

If you encounter any errors, or have additional questions, please open a Help Desk ticket by sending an email to NDAHelp@nih.gov. Please include the package id in your request, along with a brief description of the issue you are experiencing, and a copy of any errors.txt file if present.

 

Cloud Access Tools

The mission of the National Institute of Mental Health Data Archive (NDA) is to make research data available for reuse. Data collected across projects can be aggregated and made available using the GUID, including clinical data, and the results of imaging, genomic, and other experimental data collected from the same participants. In this way, separate experiments on genotypes and brain volumes can inform the research community on the over one hundred thousand subjects now contained in the NDA. The NDA’s cloud computation capability provides a framework in support of this infrastructure.

How does it work?

The NDA holds and protects rich datasets (fastq, brain imaging) in object-based storage (Amazon S3). To facilitate access, the NDA supports the deployment of data packages (created through the NDA Query tools) to an Amazon Web Service Oracle database. Originally developed for the National Database for Autism Research (NDAR), and so called miNDAR (miniature NDAR), these databases contain a table for each data structure in a package. Associated raw or evaluated data files are available via read-only access to NDA’s S3 objects. Addresses for those objects in the associated package are provided in the miNDAR table titled S3_LINKS. By providing this interface, the NDA envisions real-time computation against rich datasets that can be initiated without the need to download full data packages, with the ability to write any analyzed data directly back to the miNDAR database. This will enable the NDA to make this data available to the general research community when appropriate.

miNDARs can also be populated with your own raw or evaluated data and uploaded directly back into the NDA for a streamlined data submission directly from a hosted database.

How do I get started?

The option to launch data packages to a cloud hosted database will be available during package creation. You can deploy previously generated data packages as well as new ones.
 

Initiating miNDAR

To move NDA data to Oracle, first create a package in NDA. Then, following registration, enter the package id and credentials requested on the miNDAR tab. This will start the miNDAR creation process, which takes approximately 10 minutes. Once created, the miNDAR connect details will be emailed to you, and can be used to establish a connection with your credentials.
 

Accessing Files

Access to download data to non-AWS internet addresses is limited to 20 Terabytes over 30 days. For more detail, including examples, please read about our user download threshold.

Files included in a package are accessible from Amazon Web Services (AWS) S3 Object Storage. Each miNDAR package will have a table “S3_LINKS” table containing URIs for all objects in that package. Using direct web serivice calls to Amazon Web Service's S3 API, a third party tool, or client libraries, data from these objects can be streamed or downloaded. 

For security purposes temporary AWS credentials  are needed to access the S3 Objects. Temporary credentials are issued by authenticating with a web service using your NDA username and password.  AWS credentials can be obtained directly from the web service (see examples on our GitHub page) or from the download manager, which is available in both a GUI and command line version.

For the GUI version, go to the 'Tools' menu and select 'Generate AWS Credentials'.  

For the command line download manager, use the following syntax: 

java -jar downloadmanager.jar --username user --password pass --g 

For help with the command line download manager, use the following switches: -h, --help

The web service provides temporary credentials in three parts:

  • an access key, 
  • a secret key, 
  • and a session token

All three parts are needed in order to authenticate properly with S3 and retrieve data.  

Additionally the web service provides returns an expiration timestamp for the token in YYYY-MM-DDTHH:MM:SS-TZ format (TZ=HH:MM).  New keys can be retrieved at any time. A service oriented approach allows for implementation of pipeline procedures which can request new keys at the appropriate stage of data processing. 

Additional Help

Please see our Cloud Tutorials for a video demonstration of how to create a miNDAR, how to generate temporary security credentials, and how to use these to retrieve data.  Please contact the Help Desk with any questions.