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:
- Download the code with
git clone git@github.com: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
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/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
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.