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Welcome to DataJoint for MATLAB!

DataJoint for MATLAB is a high-level programming interface for relational databases designed to support data processing chains in science labs. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, and querying data.

For more information, see our general and MATLAB documentation pages.

Citation

  • If your work uses DataJoint for MATLAB, please cite the following Research Resource Identifier (RRID) and manuscript.

  • DataJoint (RRID:SCR_014543) - DataJoint for MATLAB (version <Enter version number>)

  • Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658

For Developers: Running Tests Locally

Click to expand details
  • Create an .env with desired development environment values e.g.
MATLAB_USER=rguzman
MATLAB_LICENSE=IyBCRUd... # For image usage instructions see https://github.com/guzman-raphael/matlab, https://hub.docker.com/r/raphaelguzman/matlab
MATLAB_VERSION=R2019a
MATLAB_HOSTID=XX:XX:XX:XX:XX:XX
MATLAB_UID=1000
MATLAB_GID=1000
MYSQL_TAG=5.7
MINIO_VER=RELEASE.2022-01-03T18-22-58Z
  • cp local-docker-compose.yaml docker-compose.yaml
  • docker-compose up (Note configured JUPYTER_PASSWORD)
  • Select a means of running MATLAB e.g. Jupyter Notebook, GUI, or Terminal (see bottom)
  • Add tests directory to path e.g. in MATLAB, addpath('tests')
  • Run desired tests. Some examples are as follows:
Use Case MATLAB Code
Run all tests run(Main)
Run one class of tests run(TestTls)
Run one specific test runtests('TestTls/TestTls_testInsecureConn')
Run tests based on test name import matlab.unittest.TestSuite;
import matlab.unittest.selectors.HasName;
import matlab.unittest.constraints.ContainsSubstring;
suite = TestSuite.fromClass(?Main, ...
    HasName(ContainsSubstring('Conn')));
run(suite)

Launch Jupyter Notebook

  • Navigate to localhost:8888
  • Input Jupyter password
  • Launch a notebook i.e. New > MATLAB

Launch MATLAB GUI (supports remote interactive debugger)

  • Shell into datajoint-matlab_app_1 i.e. docker exec -it datajoint-matlab_app_1 bash
  • Launch Matlab by running command matlab

Launch MATLAB Terminal

  • Shell into datajoint-matlab_app_1 i.e. docker exec -it datajoint-matlab_app_1 bash
  • Launch Matlab with no GUI by running command matlab -nodisplay

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Relational data pipelines for the science lab

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