Database access

Database access 2018-04-11T23:49:06+00:00

Database introduction

The database contains detailed description (metadata) for a wide selection of datasets collected in the Buzsaki Lab. The datasets are hosted on the NYU share and on CRCNS. Below you can find detailed information on accessing the database and instruction for loading the database into Matlab.

Credentials and login info

You can access and read the MySQL database with below credentials:

 IP address: 77.104.157.210:3306
 Database: buzsakid_metadata (Submit new datasets to buzsakid_submitdataset)
 Table: Datasets
 Username: buzsakid_users
 Password: BuzsakiLab9

You can access the database from anywhere, except if your local network provider is blocking MySQL traffic, which is the case for NYUMC. Computers on our access list (google spreadsheet) have been granted access. See section below for instructions for accessing with a new computer.

Registration to access the database from within NYUMC

Your computer’s IP-address has to be listed on our access list (google sheet). If your computer is not already listed, add its ip-address to the list and reach out to alexandria.help@nyumc.org to have your computer added to the firewall rule for external mySQL access by provide them with the link to the google spreadsheet.

Matlab

Setup Matlab to access the database

Follow the steps below or the detailed guides, further down the page, to access the database in Matlab

  • Verify or install the JDBC drivers.
    • If the JDBC driver for MySQL is not installed on your computer, download the driver here and follow the installation instructions below.
  • Add the JDBC driver to the MATLAB static Java class path.
    • Run the prefdir function in the Command Window. The output of this command is a file path to the MATLAB® preferences folder on your computer. For details, see prefdir.
    • Close MATLAB.
    • Navigate to the folder from step 1, and create a file named javaclasspath.txt in the folder.
    • Open javaclasspath.txt. Add the full path to the database driver JAR file in javaclasspath.txt. The full path includes the path to the folder where you downloaded the JAR file from the database provider followed by the JAR file name. The following is an example of the path: C:\DB_Drivers\mysql-connector-java-5.1.17-bin.jar. Save and close javaclasspath.txt.
    • Restart MATLAB.

Otherwise use the detailed guides below appropriate for your operating system:

Loading the database into Matlab

Download these Matlab functions to load and submit the database into Matlab. The function already contains correct credentials to access the database and load the metadata as a structure in Matlab and submit new datasets to the database.

Add your datasets to the database

You can submit your datasets to the database: buzsakid_submitdataset with this Matlab script, and I will transfer the datasets to the master database. You can do this using the credentials above. I (Peter) will be happy to set you up with your own credentials with further privileges. Please talk to me about attaining these.

Submit your datasets to the database from the website

I am currently working on an online submission form that allows you to add datasets through a web browser. You can find the form here. For this submission form, many fields are standardized and editable by the end user directly from the website. You can find the list of attributes here. Existing entries can be edited and you can submit new attributes as well.

We have a webservice sharing the Datasets folder on the NYU share. You can view and download any dataset through a browser (or from within Matlab) using a https protocol from anywhere.  You can access the datasets here: https://buzsakilab.nyumc.org/datasets/.