Skip to content
/ cobradb Public

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.

License

Notifications You must be signed in to change notification settings

SBRG/cobradb

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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

About

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.

Topics

Resources

License

Stars

Watchers

Forks

Packages

No packages published