The meta-data database contains detailed description (metadata) for a wide selection of datasets collected in the Buzsaki Lab. The datasets are hosted on a central share by NYU 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: 22.214.171.124:3306 Database: buzsakid_metadata Table: Datasets Username: buzsakid_users Password: BuzsakiLab9
You can access the database from anywhere, except if your local network provider is blocking MySQL traffic (port 3306), 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 firstname.lastname@example.org to have your computer added to the firewall rule for external mySQL access by provide them with the link to the google spreadsheet.
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
prefdirfunction in the Command Window. The output of this command is a file path to the MATLAB® preferences folder on your computer. For details, see
- Close MATLAB.
- Navigate to the folder from step 1, and create a file named
javaclasspath.txtin the folder.
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
- Restart MATLAB.
- Run the
Otherwise use the detailed guides below appropriate for your operating system:
Interacting with the database into MATLAB
We have made a database toolbox as part of the buzcode Github repository that allows you to interact with the database. There is an example script that shows basic interactions with the database.
- bz_datasbase_load: Loading the database
- bz_database_update: Update an existing dataset in the database
- bz_database_submit: Submitting a dataset to the database
- bz_database_submit_collection: Submitting a dataset collection to the database
- bz_database_credentials: database credentials
- bz_database_example_scripts: a list of example calls to the database using the functions above
You can either submit your datasets to the database: buzsakid_submitdataset with the Matlab scripts above, and I (Peter) will transfer the datasets to the master database, or I can 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
We are 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. For brain regions we are using the Allan Institute Reference Brain Atlas nomenclature and structure graph.