msimmond / proven40-moa-paper-code

Code used for analysis to support findings of the paper entitled: "Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize"

Proven40 mode-of-action paper: Analysis Code

This repo contains the code used for the analyses that support findings of the paper entitled: "Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize"

Environment set up

To run the code, you will need to recreate the analysis environment using the environment.yml file provided. To do this you will need to have conda installed. For detail instructions on how to install, visit the conda website.

Once conda is installed, the environment can be configured using:

conda env create -f environment.yml

Now activate the environment.

conda activate moa_paper

Running the analysis

The analysis is organized in three main sections. Each section includes datasets, analysis notebooks and output figures or tables:

• 1_LAB_ASSAYS includes analysis of in-vitro and in-planta assays
• 2_FIELD_TRIALS includes analysis of d15N natural abundance and 15N enrichment-dilution field experiments, as well as N fertilizer response trials at Purdue University.
• 3_ONFARM_TRIALS includes analysis of plant N status and grain yields from the on-farm field trials

Within each folder, specific analyses are contained in the jupyter notebooks (.ipynb). These have been exported as .html for preview. If you want to run the code, you will need to launch jupyter. We recommend VS Code's jupyter notebooks integration for ease of use. Notebooks are sequentially numbered according to the order they are meant to be run.

For any questions, please contact Rafael Martinez-Feria ([e-mail])