The MINE Database contains code for generating (through Pickaxe) and storing and retrieving compounds from a database. Pickaxe applies reaction rules, representing reaction transformation patterns, to a list of user-specified compounds in order to predict reactions.
For general information on MINE Databases, please consult JJeffryes et al. 2015..
Documentation is hosted at https://mine-database.readthedocs.io/en/latest/. It gives more detailed descriptions and example uses of the software.
If a conda environment is desired to be used:
conda create -n mine
conda activate mine
Then, use pip (with or without conda) to install minedatabase:
pip install minedatabase
An example file, pickaxe_run_template.py, provides a framework for running pickaxe through a python file. Feel free to download it and change it to your needs. The starting compounds, rules and cofactors, optional database information, and Pickaxe run options are specified. After running the results are stored in a specified database or written to .tsv files.
This is all explained in more detail in the documentation.
Pickaxe.py can be called independently to generate predictions with or
without database storage. To list all options call python -m minedatabase.pickaxe -h. Note that due to relative imports, it needs to be run as a module (-m flag) from the MINE-Database directory. To predict metacyc reactions for one generation on compounds in the iML1515 model one would call
python pickaxe.py -C ./data/metacyc_generalized_rules.tsv -r ./data metacyc_coreactants.tsv -g 1 -c ../example_data/iML1515_ecoli_GEM.csv