AGI-Bio

Genomic and proteomic research using the OpenCog toolset. This includes experiments in applying MOSES, PLN, pattern mining and other OpenCog components.

The MOZI.AI repositories make use of this package, and extend the current development of OpenCog-based bioinformatics tools as SingularityNET sevices.

Building and Installing

To build the AGI-Bio code, you will need to build and install the OpenCog AtomSpace first. All of the pre-requistes listed there are sufficient to also build this project. Building is as "usual":

    cd to project root dir
    mkdir build
    cd build
    cmake ..
    make -j
    sudo make install
    make -j test

Overview

The directory layout is as follows:

• bioscience - Provides the GeneNode and MoleculeNode Atom types.

• knowledge-import -- scripts for importing external knowledge bases into the AtomSpace.

• moses-scripts -- scripts for importing MOSES models; such models distinguish binary phenotype categories based on gene expression data.