You will need a running Neo4j database and login credentials of a user with write access to the database.
To populate the database, you will also need to acquire the BioCyc data files and the BRENDA text file.
The metabolike
package doesn't include the data sources since they are large and require license agreements. Please downloaded the data files and extract them for later use.
The MetaCyc (BioCyc) database is imported to the graph database using the provided SBML file and various .dat
files.
The BRENDA text file is then mapped onto the graph using common EC numbers and KEGG reaction IDs.
To install the latest stable version of the package, run the following command:
pip install metabolike
As the package is still in its early stages, it is recommended to get the latest version from GitHub:
git clone --depth 1 https://github.com/y1zhou/metabolike
To install the package, run the following command:
$ cd metabolike
$ pip install .
You can also install the package using flit:
$ flit install