carissableker / ecocyc-notebook

A neo4j server and a jupyter-notebook interface to EcoCyc 21.5

ecocyc notebook

Description

This app contains a neo4j server and a Jupyter-notebook interface to a parsed version of EcoCyc.

Starting

See docker-compose for details.

To run the first time, navigate to the folder (containing docker-compose.yml) and type:

docker-compose up

Thereafter you can use

docker-compose start

Or

docker-compose stop

Open your browser at the http://localhost:8888/?token=... link printed to the terminal. If the logs are not printed, run

docker-compose logs 

to find the correct link.

Usage

See examples/example.ipynb as an example notebook to explore the graph. You should be able to run the cells immediately.

To do list

• ...

ecocyc-notebook's Issues

Missing vertices

Add missing vertices

Graph visualization

Improve example graph visualisations

• colour vertices
• colour edges