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SBRG / cobradb

COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.
http://bigg.ucsd.edu
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database python sqlalchemy

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COBRAdb

COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is available under the MIT license.

Installation

COBRAdb requires PostgreSQL, Python 2.7 or 3.6+, and a number of Python packages listed in setup.py.

  1. Install and set up PostgreSQL. This process varies from platform to platform, but the best place to start in the PostgreSQL documentation.

  2. Set up your configuration. Copy the file settings.ini.example and rename it settings.ini. The example file includes descriptions of each setting. You can use the settings file from BiGG Models as a guide: https://github.com/SBRG/bigg_models_data

  3. Install COBRAdb and dependencies.

python setup.py install
# OR
python setup.py develop
# OR
pip install -e .
  1. Load the database by calling the script bin/load_db.
bin/load_db --drop-all