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# Access openBIS from MATLAB
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## Preamble
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openBIS is a research data management system developed by ETH SIS. Data stored in openBIS can be accessed directly via the web UI or programmatically using APIs. For example, pyBIS is a project that provides a Python 3 module for interacting with openBIS.
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MATLAB is a high-level numerical computing environment that is popular in many areas of science. It is therefore desirable to have the possibility to access data in openBIS directly from MATLAB. This repository provides a MATLAB script that demonstrates how this can be achieved by calling the pyBIS module directly from MATLAB.
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[openBIS](https://wiki-bsse.ethz.ch/display/bis/Home) is a research data management system developed by [ETH SIS](https://sis.id.ethz.ch/). Data stored in openBIS can be accessed directly via the web UI or programmatically using APIs. For example, [pyBIS](https://sissource.ethz.ch/sispub/pybis) is a project that provides a Python 3 module for interacting with openBIS.
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[MATLAB](https://ch.mathworks.com/products/matlab.html) is a high-level numerical computing environment that is popular in many areas of science. It is therefore desirable to have the possibility to access data in openBIS directly from MATLAB. This repository provides a MATLAB script that demonstrates how this can be achieved by calling the pyBIS module directly from MATLAB.
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## Setup
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#### OS X
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On OS X, the setup has been tested with a Miniconda Python distribution.
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1. Download and install Miniconda3 (using Python 3.6 version)
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1. Download and install [Miniconda3](https://conda.io/miniconda.html) (use the Python 3.6 version)
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2. Install pyBIS with pip: `pip install pybis`
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3. Open MATLAB and set the Python executable (modify path according to your system): `pyversion /Users/Henry/miniconda3/bin/python`
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#### Windows 10
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On Windows using the Anaconda or Miniconda approach did not work (For some reason, MATLAB could not find the Python modules). On the other hand, using the standard Python 3.6 installation worked.
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1. Download and install Python 3.6 (from python.org)
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On Windows using the Anaconda or Miniconda approach did not work (for some reason, MATLAB could not find the Python modules). On the other hand, using the standard Python 3.6 installation worked.
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1. Download and install [Python 3.6](https://www.python.org/downloads/)
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2. During the installation, make sure Python is added to the Path and registered as default Python interpreter.
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3. Open a command prompt and install pyBIS with pip: `pip install pybis`
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3. Open MATLAB and set the Python executable: `pyversion 3.6`
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... | ... | @@ -25,4 +25,4 @@ On Windows using the Anaconda or Miniconda approach did not work (For some reaso |
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Please have a look at the script [MatlabPybis_example.m](https://sissource.ethz.ch/hluetcke/matlab-openbis/blob/master/MatlabPybis_example.m) for a documented example. The pyBIS documentation is available here: https://sissource.ethz.ch/sispub/pybis/blob/master/src/python/PyBis/README.md
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## Outlook
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In the future, it is planned to develop this project into a fully featured MATLAB toolbox that emulates the features of pyBIS. |
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\ No newline at end of file |
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In the future, it is planned to develop this project into a MATLAB toolbox that emulates the features of pyBIS. |
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\ No newline at end of file |