MechRepoNet for Alzheimer's Disease

This repository starts the process of using MechRepoNet and it's various endpoints to probe potential treatments for Alzheimer's Disease.

This repo uses the outputs of both MechRepoNet and MRN new endpoints. This repo should be placed in the same directory as MRN new endpoints as it simlinks to some of the param files found in that repository.

JSON files in the 0_data/manual directory may need to be edited to provide the proper paths for the data used from the MechRepoNet and pipeline

Organization

This repository is organized as follows.

/0_data           # Contains data needed to for use within scripts
    manual        # Data built manually. Most will be included, unless built from proprietary source
    external      # Data acquired from external sources. Not included, but scripts will provide most
/1_code           # Contains all code for running the pipeline. Scripts and notebooks are numbered in order they should be run.
    tools         # contains tools for building
/2_pipeline       #  Output folder for pipeline. Not included with repo

Setting up the environment

This repo uses essentially the same environment as MechRepoNet. Please use the requirements.txt from that repository.

Additional requriement above MechRepoNet: $ pip install fpdf

Location

This repo and all associated datafiles are located at /gpfs/group/su/mike/MRN_AD