Language-oriented rule-based reaction network generation and analysis: Description of RING

The input and output formats, and the structure of Rule Input Network Generator (RING), a computational tool for generation and analysis of complex reaction networks, are described with reference to the underlying algorithms from Cheminformatics and graph theory. RING consists of three modules: (a) a compiler that translates inputs written as a program in an English-like reaction language into internal representations and instructions, (b) a network generator that constructs an exhaustive reaction network from reaction rules and initial reactants specified, and (c) a post-processing module that can extract pathways, mechanisms, or lumps from the network based on user-specified instructions. RING can be used, in a rule-based manner, for constructing a large and complex reaction network from a set of elementary/overall reaction rules, and for elucidating transformations occurring in these networks through identifying pathways and mechanisms to specified products. RING is available open under GNU Lesser GPL.

► New open source computational tool for network generation and analysis. ► Rule-based framework for constructing and topological analysis of complex networks. ► Domain-specific language interface with syntactic and semantic chemistry-specific error catching. ► Flexible and versatile network generation tool. ► Tool for network analysis in conjunction with experimental and computational data.