DRRS

DRRS (Drug repositioning recommendation system)

DRRS, a novel computational drug repositioning method using low-rank matrix appropriation and randomized algorithm, is used for predicting drug indications by integrating related data sources and validated information of drugs and diseases.The command-line version of DRRS can be run on a Microsoft Windows or a Linux platform. Here, we provide software and the used datasets for download.

1. Software

(1) DRRS_W: the DRRS program running on Windows;
(2) DRRS_L: the DRRS program running on Linux;

2. Datasets

DRRS can conduct drug-disease predictions on three datasets: Fdatasets, Cdatasets and DNdatasets.

(1)Fdatasets
- ① DrugSim.txt: drug similarity file;
- ② DiseaseSim.txt: disease similarity file;
- ③ DiDrA.txt: disease-drug association file;
(2) Cdatasets
(3) DNdatasets
Tips: Cdatasets and DNdatasets also contain the similarity and association matrix files.

Read Me

The command-line version of DRRS can be run on a Microsoft Windows or a Linux platform.

Windows
Linux

MATLAB Compiler Runtime (MCR) is a runtime environment that allows the execution of MATLAB-based applications.

MCR Windows version [R2012b (8.0) 32-bit] is required to be installed before running DRRS, and MCR_R2012b_win32_installer.exe can be downloaded from the MathWorks web site by clicking on the following link: http://www.mathworks.com/products/compiler/mcr.html

Step 1: Install MATLAB Compiler Runtime (MCR)

(1) Run MCR_R2012b_win32_installer.exe;
(2) Add the path MCR_Path\runtime\win32 to System Environment Variable, where MCR_Path is the installation directory of MCRInstaller. (The default installation directory of MCRInstaller is C:\Program Files (x86)\MATLAB\MATLAB Compiler Runtime\v80)

Step 2: Run program DRRS_W.exe

(1) Open a Dos command prompt shell window;
(2) Change the working directory to that DRRS_W.exe and dataset files (DrugSim.txt, DiseaseSim.txt and DiDrA.txt) are stored;
(3) Enter command:
- DRRS_W.exe DrugSim.txt DiseaseSim.txt DiDrA.txt
After running DRRS_W.exe, file Result_dr_Mat.txt is generated as the output file. Here, Result_dr_Mat.txt is the completed disease-drug association matrix file containing predicted scores for unknown disease-drug associations.

Example

(1) Download DRRS_W.exe, MCR_R2012b_win32_installer.exe and Fdatasets.zip to E:\DRRS, unzip Fdatasets.zip and put files DrugSim.txt, DiseaseSim.txt and DiDrA.txt in E:\DRRS;
(2) Run MCR_R2012b_win32_installer.exe, and install MCR to E:\MCR\;
(3) Add E:\MCR\V80\runtime\win32 to System Environment Variable;
(4) Open a Dos command window and type the below commands;
- ① cd E:\DRRS;
- ② DRRS_W.exe DrugSim.txt DiseaseSim.txt DiDrA.txt;
- * The computational results of this example depend on the random numbers generated, which may not be exactly the same as those shown in the manuscript submitted to Bioinformatics.

MCR Linux version [R2012b (8.0) 64-bit] is required to be installed before running DRRS, and MCR_R2012b_glnxa64_installer.zip can be downloaded from the MathWorks web site by clicking on the following link: http://www.mathworks.com/products/compiler/mcr.html

Step 1: Install MCR (Matlab Component Runtime);

# Enter the below commands:
(1) mv MCR_R2012b_glnxa64_installer.zip /tmp
(2) cd /tmp
(3) unzip MCR_R2012b_glnxa64_installer.zip -d MCRInstaller
(4) cd MCRInstaller
(5) ./install -mode silent -agreeToLicense yes
(6) vi /etc/profile
- # add new environmental variables to /etc/profile
- export MCR_HOME=/usr/local/MATLAB/MATLAB_Compiler_Runtime
- export LD_LIBRARY_PATH=$MCR_HOME/v80/runtime/glnxa64:$MCR_HOME/v80/bin/glnxa64:$MCR_HOME/v80/sys/java/jre/glnxa64/jre/lib/amd64/server:$MCR_HOME/v80/sys/os/glnxa64:$MCR_HOME/v80/sys/java/jre/glnxa64/jre/lib/amd64:$MCR_HOME/v80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads
- export XAPPLRESDIR=$MCR_HOME/v80/X11/app-defaults
(7) source /etc/profile # # reload /etc/profile, and check if the new environmental variables have been set correctly (e.g., use the env command).

Step 2: Run program DRRS_L

(1) Change the working directory to that DRRS_L and dataset files (DrugSim.txt, DiseaseSim.txt and DiDrA.txt) are stored;
(2) Enter command:
- # the libXmu.so.6 is required before running DRRS_L
- ./DRRS_L DrugSim.txt DiseaseSim.txt DiDrA.txt
After running DRRS_L, file Result_dr_Mat.txt is generated as the output file. Here, Result_dr_Mat.txt is the completed disease-drug association matrix file containing predicted scores for unknown disease-drug associations.

Example

We take the prediction on Fdatasets as an example. DRRS_L, MCR_R2012b_glnxa64_installer.zip and Fdatasets.zip are downloaded and stored in /tmp.

(1) cd /tmp
(2) unzip MCR_R2012b_glnxa64_installer.zip -d MCRInstaller
(3) cd MCRInstaller
(4) ./install -mode silent -agreeToLicense yes
(5) add new environmental variables to /etc/profile as shown in Step1, reload /etc/profile and check if the new environmental variables have been correctly by using the env command;
(6) unzip Fdatasets.zip, and put DrugSim.txt, DiseaseSim.txt and DiDrA.txt in /tmp;
(7) cd /tmp
(8) ./DRRS_L DrugSim.txt DiseaseSim.txt DiDrA.txt

About

DRRS is a novel computational method to predict potential drug-disease associations.

Questions and comments on the tool and suggestions for improvement to the website are always welcome.

Please contact:

Yaohang Li: yaohang@cs.odu.edu

Jianxin Wang: jxwang@mail.csu.edu.cn