The new BiGG Models website server
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README.md

BiGG Models

Installation

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: 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 git@github.com: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/yayfmcrsrtrcypw/AACDoew92pCYlSJa8vCs5rSMa?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.