Welcome to MINE-Database’s Documentation!


MINE-Database, also referred to as Pickaxe, is a python library allows you to efficiently create reaction networks based on a set of reaction rules.

Some common use cases:

  1. Predicting promiscuous enzymatic reactions in biological systems.

  2. Searching for potential novel reaction pathways from starting compound(s) to target compound(s).

  3. Annotating possible structures for unknown peaks in metabolomics datasets.

  4. Predicting spontaneous chemical reactions which may be diverting flux from a pathway of interest.

  5. Specifying custom reaction rules to extend reaction networks to include chemical reactions.

In all of these cases, you supply pickaxe with a set of starting compounds (as SMILES strings) and which set of reaction rules you would like to useand then Pickaxe does the rest. Pickaxe creates a network expansion by applying these reaction rules iteratively to your starting set of compounds, going for as many generations as you specify. There are many more advanced options and customizations you can add as well.

Getting Started

To get started, see Installation.

You can run pickaxe in two ways, in command-line mode (Running Pickaxe via Command Line) or using a template file (recommended) (Running Pickaxe). Running Pickaxe also provides information about different compound filters you can apply to your pickaxe expansions.

For a list of inputs required for pickaxe, see Generating Pickaxe Inputs.

To learn how to create your own custom filters, see Custom Filters.

An API reference is provided at API Reference if you need to see implementation details.

Finally, if you find yourself needing help or have feedback for us, please see Support!