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.
Bibliographical noteFunding Information:
The authors would like to thank Prof. Eric Van Wyk and Ted Kaminski, Department of Computer Science and Engineering, University of Minnesota, for helpful suggestions on computer science algorithms and collaboration on developing the reaction language for RING. Financial support from the Initiative for Renewable Energy (Large Grant: RL-0004-09 ) at the University of Minnesota , the National Science Foundation Emerging Frontiers in Research and Innovation program , grant # 0937706 is gratefully acknowledged. A.B. was supported as part of the Catalysis Center for Energy Innovation, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Award number DE-SC0001004.
- Domain specific language interface
- Mechanism elucidation
- Pathway analysis
- Reaction network analysis
- Rule-based network generation