Centrifuge

Let's put these networks through our centrifuge? Sure, will do!

The "Centrifuge" DSL is a modelling tool for networks.

Features

• Import networks from GraphML files with readNetwork function. Supply a parser function for network nodes.
• Split, merge or remove vertices.
• Induce subnetworks.
• Generate VHDL circuit descriptions for simulation.

Try "Centrifuge" interactively in GHCi

Module Centrifuge.DSL.Protein contains a trivial instantiation of the "Centrifuge" DSL tied up to protein networks (valuable for drug discovery). Here is an example session.

Run GHCi with stack:

> stack ghci

Enable the OverloadedStrings extension to use ByteString literals

> :set -XOverloadedStrings

Import the network from GraphML file

> g1 <- readProteinNetwork "examples/graphs/fdl_17.graphml"
> print g1
[("A","B"), ("B","C"), ("B","D"), ("C","E"), ("D","E")]

Vertex merging

> g2 = mergeVertices ["C","D"] "CD" g1
> print g2
[("A","B"), ("B","CD"), ("CD","E")]

Vertex splitting

> g3 = splitVertex "CD" ["C","D"] g2
> print g3
[("A","B"), ("B","C"), ("B","D"), ("C","E"), ("D","E")]

Subgraph induction

> relevantProtein p = p ‘notElem‘ ["A","D","CD"]
> induce relevantProtein g3
[("B","C"), ("C","E")]

VHDL outout

> writeVHDL g3 "circuit.vhdl"

More info

This repo is meant to be an accompanying material for "Language and Hardware Acceleration Backend for Graph Processing" FDL'17 paper.

VHDL code generation is a port of a corresponding pangraph module.

Graph manipulation and transformation are performed be means of Algebraic graphs.