PyBEL Tools is a suite of tools built on top of PyBEL to facilitate data management, integration, and analysis.
This package was developed at Fraunhofer SCAI with support from the IMI projects: AETIONOMY and PHAGO.
PyBEL Tools can be installed easily from PyPI with the following code in your favorite terminal:
$ python3 -m pip install pybel_toolsor from the latest code on GitHub with:
$ python3 -m pip install git+https://github.com/pybel/pybel-tools.git@developBefore running the service, some data can be pre-loaded in your cache.
The Selventa Small Corpus and Large Corpus are two example BEL documents distributed by the OpenBEL framework. They are good examples of many types of BEL statements and can be used immediately to begin exploring. Add -v for more logging information during compilation. This is highly suggested for the first run, since it takes a while to cache all of the namespaces and annotations. This only has to be done once, and will be much faster the second time!
Small Corpus:
$ python3 -m pybel_tools ensure small_corpus -vLarge Corpus:
$ python3 -m pybel_tools ensure large_corpus -vA single network stored as a PyBEL gpickle can quickly be uploaded using the following code:
$ python3 -m pybel_tools io upload -p /path/to/my_network.gpickleMore examples of getting data into the cache can be found here.
PyBEL Tools deploys a Flask web application that allows you to interact with your networks and apply filters/algorithms.
Multiple services are available. Use --help for a description. To run the web services, type:
$ python3 -m pybel_tools webBy default, Flask deploys on localhost at port 5000. These can be changed respectively with the --host and --port arguments. Additionally, logging can be shown with -v. More documentation on the web services can be found here.
- Documentation at http://pybel-tools.readthedocs.io
- Cookbook at https://github.com/pybel/pybel-notebooks
- Documented on Read the Docs
- Versioned on GitHub
- Tested on Travis CI
- Distributed by PyPI
- Chat on Gitter