This repository contains code developed by the Gulf Coast Consortia Combinatorial Drug Discovery Program (CDDP) at Texas A&M Center – Institute of Bioscience and Technology at the Texas Medical Center in Houston, Texas.
The code is experimental and not thoroughly tested across all machines. If you get an error, or something doesn't seem to be working, PLEASE LET US KNOW. Most of the code here is written in Python and Pipeline Pilot, although there are some R scripts that are automated using Pipeline Pilot (Biovia).
Contact: Reid T. Powell repowell@tamu.edu
README This file. LICENSE How this code is licensed. USAGE Instructions to replicate the finds of the study Images/ Place holder folder, images availbe from link below Code/ Jupyter notebooks and Pipeline Pilot scripts. Metadata/ Experimental metadata
Image files available at: https://drive.google.com/drive/folders/1SWa5IZubeDNOrd9tkwbkrp3sJEmViWFW
System requirements: This code was not thoroughly tested on a wide range of machines. The system configuration that was used to perform all analysis/benchmarking was performed on a Dell PowerEdge R740xd server running Windows Server 2016 standard edition and equipped with: dual 3.3 Ghz Xeon Gold 6246 CPUs [Intel], 192 Gb DDR5 RAM, and a NVIDIA Tesla V100 32Gb purchased from Dell EMC using funds from the CPRIT CFSA RP150578. All scripts have been tested on a machine running Windows 2016 and Windows 10, no other operating systems have been tested. DNN feature embeddings have been optimized to run on a PC equipped with a GPU, however, this is not required. • Python 3.8 and libraries, Python 2.7 not supported o Required python libraries: Pythorch - https://pytorch.org/. Download and manipulate neural networks Numpy – https://www.numpy.org. Used for image manipulation o Optional python libraries PyQT5 - https://pypi.org/project/PyQt5/5.10/. Interactive file browsing • R 3.4+ o Required R Libraries Caret - https://topepo.github.io/caret/. kNN functions e1071 - https://cran.r-project.org/web/packages/e1071/index.html. SVM functions • Pipeline Pilot 2018 Server o Scripts developed using Pipeline Pilot require a paid license that may be purchased from: https://www.3ds.com/products-services/biovia/products/data-science/pipeline-pilot/. Installation instructions are provided with purchase. Must configure R and ImageJ integration