mgiammar / mine-database

Metabolic In silico Network Expansion (MINE) Database Construction and DB Logic

MINE Databases

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.

Documentation

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.

Installation

MINE-Database requires the use of rdkit, which currently is unavailable to install on pip. Thus, we recommend you use conda to create a new environment and then install rdkit into that environment before proceeding:

conda create -n mine

conda activate mine

conda install -c rdkit rdkit

Then, use pip (in your conda environment) to install minedatabase:

pip install minedatabase

Running Pickaxe

Running Pickaxe through a python file (recommended)

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 command-line usage (not recommended - see above section)

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