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.
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:
- Download the code with
git clone [email protected]:SBRG/bigg_models.git
cd bigg_models
- Install with
python setup.py develop
(may need to sudo or add --user) - Generate the PostgreSQL indices by running
bin/make_database_indices
. - Generate the static models by running
bin/make_all_static_models
. - Start the server with
python -m bigg_models.server --port=8910
BiGG Models can also be installed with Docker. Everything you need is here, thanks to @psalvy:
https://github.com/psalvy/bigg-docker
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.
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
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: http://bigg.ucsd.edu/license.