bigg_models

BiGG Models is a website for browsing gold-standard genome-scale models, described in our publication here:

King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015). BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucl Acids Res. doi:10.1093/nar/gkv1049.

This repository includes the web server and front-end for BiGG Models. The database is managed by COBRAdb. You can see our plans for new BiGG Models features in the Development Roadmap.

Installation

To install BiGG Models, first, follow the OME installation instructions: https://github.com/SBRG/ome/blob/bigg/INSTALL.md

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

1. Download the code with git clone [email protected]:SBRG/bigg_models.git
2. cd bigg_models
3. Install with python setup.py 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:

https://github.com/psalvy/bigg-docker

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 http://bigg.ucsd.edu. 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:

https://www.dropbox.com/sh/ye05djxrpxy37da/AAD6GrSRTt4MRfuIpprlnLYba?dl=0

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.

License

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: http://bigg.ucsd.edu/license.