Genome Explorer

This is the source code of the software tool for paper:

GPU Accelerated Browser for Neuroimaging Genomics

Bob Zigon, Huang Li, Xiaohui Yao, Shiaofen Fang, Mohammad Al Hasan, Jingwen Yan, Jason H. Moore, Andrew J. Saykin, Li Shen, for the Alzheimer's Disease Neuroimaging Initiative

How to Run

You can either compile it from the source code or download the binary from here. An example dataset is included in the binary zip file.

software manual

If you want to compile it from the source code, follow the 'How to Compile' section.

How to Compile

Dependencies:

• Qt 5.7 or later
• VTK 7.0.0 or later
• CUDA 8.0
• Windows 7 or later

Client:

1. Load BECA.pro with Qt Creator
2. Set VTK_ROOT and VTK_MAIN_VERSION in file vtk.pri VTK_ROOT is the path where VTK is installed VTK_MAIN_VERSION is the version number of VTK
3. Click menu Build -> Build All

Server:

1. Load libplugins\libgenomeexplorer\calculation_backend\BServerExperiments.sln with Visual Studio 2015 or later
2. Build 'BServer'

Follow the instruction in software manual to run it.

Input Data Format

Input data format

If you want to use the genome explorer with custom data instead of the example data in the binary zip file, you can prepare your data in the following format.

Genotype data: (example_data/genotype.txt)

You can load this file with Excel. Each row is a subject, and each column is a SNP

Phenotype data: (example_data/phenotype.bin)

This file is a N by M matrix in binary format. The first 8 bytes are two 32bit integers indicating the number of subjects (N) and the number of measurements (M) for each subject, which is followed by NxM 32bit float-point numbers. The matrix is written in row major format.