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Update README.md
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greglandrum authored Aug 31, 2023
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Expand Up @@ -10,10 +10,10 @@ This repo contains the code and datasets for the publication
# Data and results

## Directories:
- datasets: contains the assay datasets exported from ChEMBL30 as well as the results of running SIMPD on the assay datasets. There's also a data catalog description for the intake package in here
- datasets: contains the Ki datasets exported from ChEMBL32 as well as the results of running SIMPD on the assay datasets. There's also a data catalog description for the intake package in here

# Jupyter Notebooks
- 01_Get_ChEMBL30_Bioactivity_Data_assays.ipynb : export the raw ChEMBL assay datasets from ChEMBL
- 01_Get_ChEMBL32_Bioactivity_Data_assays.ipynb : export the raw ChEMBL Ki datasets from ChEMBL
- 02_ChEMBL_ML_experiments.ipynb : analysis of the results of the ML experiments on the ChEMBL Datasets

# Python files
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- run_chemblassay_ml_nogap.py : script to run the ML experiments on the base assay data
- run_chemblassay_ga_nogap.py : script to run SIMPD on the base assay data
- run_chemblassay_ml_moo_nogap.py : script to run the ML experiments on the SIMPD results
- create_simpd_output_chemblassay.py : script to create CSV files with the final SIMPD datasets. This is what ends up in the datasets/chembl_SIMPD directory
- create_simpd_output_chemblKi.py : script to create CSV files with the final SIMPD datasets. This is what ends up in the datasets/chembl_SIMPD directory



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