LabbookDB

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This package contains a relational database structure for life science research, and a number of functions to conveniently add and retrieve information - and generate summaries. The core concept of LabbookDB is that most of the information classically tracked in a lab book can be more efficiently and more reliably stored in a relational database.

In comparison to a paper notebook, an electronic lab book is:

• More easily stored
• More easily shared
• More easily backed up

In comparison with other electronic formats based on a document concept, a database of experimental metadata is:

• More easily browsed
• More easily queried
• More easily integrated into data analysis functions

Presentations

Video

* `LabbookDB - A Relational Framework for Laboratory Metadata <https://www.youtube.com/watch?v=FKWznqP6rcE>`_, at SciPy 2017 in Austin (TX,USA).

Publications

• LabbookDB - A Wet-Work-Tracking Database Application Framework <https://www.researchgate.net/publication/319855508_LabbookDB_A_Wet-Work-Tracking_Database_Application_Framework>_, in Proceedings of the 15th Python in Science Conference (SciPy 2017).

Installation

Gentoo Linux

LabbookDB is available for Portage (the package manager of Gentoo Linux, derivative distributions, as well as BSD) via the `Gentoo Science Overlay <https://github.com/gentoo/sci/>`_.
Upon enabling the overlay, the package can be emerged:

.. code-block:: console

    emerge labbookdb


Python Package Manager (Users)

Python's setuptools allows you to install Python packages independently of your distribution (or operating system, even). This approach cannot manage any of our numerous non-Python dependencies (by design) and at the moment will not even manage Python dependencies; as such, given any other alternative, we do not recommend this approach:

.. code-block:: console

git clone [email protected]:TheChymera/LabbookDB.git
cd LabbookDB
python setup.py install --user

Python Package Manager (Developers)

Python's `setuptools` allows you to install Python packages independently of your distribution (or operating system, even);
it also allows you to install a "live" version of the package - dynamically linking back to the source code.
This permits you to test code (with real module functionality) as you develop it.
This method is sub-par for dependency management (see above notice), but - as a developer - you should be able to manually ensure that your package manager provides the needed packages.

.. code-block:: console

    git clone [email protected]:TheChymera/LabbookDB.git
    cd LabbookDB
    mkdir ~/.python_develop
    echo "export PYTHONPATH=\$HOME/.python_develop:\$PYTHONPATH" >> ~/.bashrc
    echo "export PATH=\$HOME/.python_develop:\$PATH" >> ~/.bashrc
    source ~/.bashrc
    python setup.py develop --install-dir ~/.python_develop/

Example Input
-------------

LabbookDB is designed to organize complex wet work data.
We publish example input to generate a relationship-rich database in a separate repository, `demolog <https://bitbucket.org/TheChymera/demolog>`_.

Dependencies
------------

* `Argh`_
* `Pandas`_
* `simplejson`_
* `SQLAlchemy`_

Optional Dependencies for Introspection

• Sadisplay_

Optional Dependencies for PDF Protocol Generation

* `TeX Live`_

Optional Dependencies for Plotting
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* `BehavioPy`_
* `Matplotlib`_


.. _Argh: https://github.com/neithere/argh/
.. _BehavioPy: https://github.com/TheChymera/behaviopy
.. _Matplotlib: https://matplotlib.org/
.. _Pandas: http://pandas.pydata.org/
.. _Sadisplay: https://bitbucket.org/estin/sadisplay/wiki/Home
.. _simplejson: https://github.com/simplejson/simplejson
.. _SQLAlchemy: http://www.sqlalchemy.org/
.. _TeX Live: https://www.tug.org/texlive/