CuDDI

CuDDI: A CUDA-based application for identifying drug-drug interaction related information from PubMed literature

Developed by Aditya Chandra Vothgod Ramachandra, Yin Lu, Yi-Cheng Tu, and Feng Cheng

Instructions for CuDDI:

the process of the CuDDI application is classified into three modules:

Module 1: downloading DDI related substances,

Module 2: random sampling and p-value calculation, and

Module 3:exporting the significant compound and protein terms.

Module 1 is performed in step 1 and Modules 2 and 3 are performed in step2.

The detailed commands to compile and execute source code are as follows:

Here, we use Ibuprofen as an example.

1. Module 1

python step_1_download_Substance.py drugNameList_original para.txt

In this step, please make sure that the Biopython package is installed.

There are five output files which are:

ibuprofen_PMID_Substances.txt

ibuprofen_result_1_compounds.txt (DDI-related)

ibuprofen_result_1_proteins.txt (DDI-related)

ibuprofen_result_2_compounds.txt (DDI-unrelated)

ibuprofen_result_2_proteins.txt (DDI-unrelated)

2. Modules 2 and 3

2.1 CUDA-based implementation for Modules 2 and 3.

Compile the source code in the computer which has NVIDIA GPU by using the command:

nvcc step_2_randomSampling_pValue_output.cu -o step_2_randomSampling_pValue_output -Wno-deprecated-gpu-targets

Run the executable file:

step_2_randomSampling_pValue_output ibuprofen_result_1_compounds.txt ibuprofen_result_2_compounds.txt ibuprofen_result_1_proteins.txt ibuprofen_result_2_proteins.txt para.txt "Ibuprofen"

2.2 Python-based implementation for Module 2 and Module 3.

In this step, please make sure that the scipy and numpy packages are installed.

Run the python script:

python step_2_randomSampling_pValue_output.py ibuprofen_result_1_compounds.txt ibuprofen_result_2_compounds.txt ibuprofen_result_1_proteins.txt ibuprofen_result_2_proteins.txt para.txt "Ibuprofen"

There are four output files containing the compounds and proteins information for Ibuprofen related DDI which are:

Ibuprofen_temp_result1_Substance_compounds_cutoff_1.txt

Ibuprofen_temp_result1_Substance_compounds_cutoff_1_p_0.1.txt

Ibuprofen_temp_result1_Substance_proteins_cutoff_1.txt

Ibuprofen_temp_result1_Substance_proteins_cutoff_1_p_0.1.txt