README

Splash is a header-only parallel framework that enables fast construction of MI-based gene regulatory networks (GRN). Splash is implemented in C++ and is parallelized for multi-core and MPI multi-node environments. It is designed to reconstruct networks in unsupervised and semi-supervised manners.

Splash includes the following functionalities:

• Parallel IO to read data using exp and HDF5 formats
• Computation kernels for computing Pearson correlation metrics.
• Computation kernels to compute MI using Adaptive Paritioning and B-spline methods.
• Computation kernels to compute Stouffer and CLR transformation of correlation measures.
• ... and many more.

Installation

At the moment the software is software is released as source code, so it is necessary to compile on your own system.

Pre-requisites

Below are the prerequisites. The example code are for ubuntu and debian distributions

• A modern c++ compiler with c++11 support. Supports Gnu g++, clang++ and Intel icpc.

          sudo apt install build-essential

• MPI, for example openmpi or mvapich2

          sudo apt install openmpi

• cmake, and optionally cmake GUI

          sudo apt install cmake cmake-curses-gui

• HDF5

          sudo apt install hdf5-helpers hdf5-tools libhdf5-dev

Usage

Please refere to MCPNet repositories for examples of how Splash can be used to construct