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.
At the moment the software is software is released as source code, so it is necessary to compile on your own system.
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
Please refere to MCPNet repositories for examples of how Splash can be used to construct