Date: 6 October 2016

This directory includes source code associated with the publication "Stepwise Distributed Open Innovation Contests for Software Development - Acceleration of Genome-Wide Association Analysis".

LICENSE

All source code here is released under the GNU General Public License Version 2 (GPL2). See COPYING.txt for a copy of the license.

PREREQUISITES

Codes have been tested on Red Hat Enterprise Linux 6 with gcc 4.4.7, 32 GB RAM. We cannot guarantee compilation or execution in other environments.

CONTENTS

The codes are contained in subdirectories. See the manuscript for more detailed descriptions of each code.

C1: A top-scoring TopCoder contest submission, amended to read PLINK binary filesets
C2: C1, amended to accelerate the initial reading of PLINK binary data
C3: C2, with additional multithreading
plink-flr: PLINK 1.07 source code, amended to include the contest-winning logistic regression code

An example PLINK fileset is included in the t/ subdirectory, containing synthetic data for N=6000 individuals, M=7000 markers, P=1 phenotype and C=5 covariates.

RUNNING

A 'test' makefile target is provided that will execute the codes on the example PLINK fileset.

To run the codes:

For C1:
cd C1
make test

For C2:
cd C2/venco
make test

For C3:
cd C3/venco
make test

For plink-flr:
cd plink-flr
make test