Pickaxe

This repo contains the code used to generate the data and figures for the Pickaxe paper. Pickaxe is a compound/reaction generation tool that utilizes reaction rules to construct a network of novel compounds and reactions. This tool was used to generate MINEs for the MINE database and the code can be found here.

Repo Structure

This repo is structured into folders containing code and analysis.

Figure 3

• Generation code for exponential growth is found in fig3_gen_exp_growth/run_files/mem_lt300_100r.py
• Generation code for runtime is found in fig3_gen_exp_growth/analysis/benchmarks.ipynb
• Plotting code is found in fig3_gen_exp_growth/analysis/fig3_plot.ipynb

Figure 4

• Generation code is found in fig4_YMDB_cutoff/
• Results are stored in a mongo database.
• Analysis code is found in fig4_gen/analysis/tani_both_analysis.ipynb

Figure 5

• Generation code is found in fig5_sample/C4C8_2k_Conly/runs/
• Results are stored in mongo databases.
• Analysis code is found in fig5_sample/C4C8_2k_Conly/analysis/run_production_sampling2k.ipynb

Figure 6

• Generation code is found in fig6_ecocyc_metabolomics/laptop/analysis/ecoli_metabolomics_gen.ipynb
• Results are stored in a mongo database.
• Analysis code is found in fig6_ecocyc_metabolomics/laptop/analysis/ecoli_metabolomics_analysis.ipynb
• The Analysis code can be sped up using feasibility_first_gen.py, feasibility_second_gen_gen2.py, and get_physiological_dgs.py
• The code is also repeated on a supercomputer found in fig6_ecocyc_metabolomics/supercomputer

Software Requirements

The code in this example requires the minedatabase package as well as some additional packages for different filters.

minedatabase Installation

Installation via pip

pip install minedatabase

Installation from source via conda

git clone https://github.com/tyo-nu/MINE-Database

then within the MINE-Database folder

conda env create -f environment.yml conda activate minedatabase

eQuilibrator Installation

The thermodynamics filters require the use of eQuilibrator. This can be installed via conda

conda install -c condaforge equilibrator-api

DeepRFC Installation

The feasibility filters require the use of DeepRFC, which can be installed by following the instructions found on their website.

MongoDB Installation

These examples rely on using a mongo database, either remote or local. To install this database, download the installer and follow the instructions.

PyMongo provides methods to interact with the database via python code.