The new BiGG Models website server
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bigg_models new headers Nov 23, 2016
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BiGG Models


BiGG Models is a web front end for genome-scale models stored using the OME Framework.

To install BiGG Models, first, follow the OME installation instructions:

Then, do the following to get BiGG Models up and running:

  1. Download the code with git clone
  2. cd bigg_models
  3. Install with python develop (may need to sudo or add --user)
  4. Generate the PostgreSQL indices by running bin/make_database_indices.
  5. Generate the static models by running bin/make_all_static_models.
  6. Start the server with python -m bigg_models.server --port=8910

Alternative installation: Docker

BiGG Models can also be installed with Docker. Everything you need is here, thanks to @psalvy:

Testing BiGG Models

Tests are run in both the ome and BiGG Models codebases using pytest. Running py.test with ome will create a temporary database and load it with a few simple test models. These tests can be run at any time. Running py.test with BiGG Models will run a series of test that are specific to the models currently available at These tests can only be run after the whole database is loaded.

Dumping and restoring the database

The latest database dumps are available in this Dropbox folder:

We generally dump the database with this command:

pg_dump -Fc bigg > bigg_database.dump

And then restore like this:

pg_restore -c -d bigg bigg_database.dump

Generate a schema browser

Install and run schemaSpy. For example, here are the Mac OS X instructions:

brew install graphviz

brew tap gbeine/homebrew-java
brew install postgresql-jdbc

java -jar bin/schemaSpy_5.0.0.jar -t pgsql -db bigg -u username -s public \
  -o docs/schema -host localhost -port 5432 \
  -dp /usr/local/Cellar/postgresql-jdbc/9.3-1102/libexec/postgresql-9.3-1102.jdbc3.jar

Then open docs/schema/index.html in a web browser.


This codebase is released under the MIT license. The license information for the BiGG Models website hosted at SBRG and the associated models can be found here: