A modular computational tool for automated generation and rule-based post-processing of reaction systems in biomass conversion is presented. Cheminformatics and graph theory algorithms are used to generate chemical transformations pertaining to heterogeneous and homogeneous chemistries in the automated rule-based network generator. A domain-specific language provides a user-friendly English-like chemistry specification interface to the network generator. A rule-based pathway analysis module enables the user to extract and query pathways from the reaction network. A demonstration of the features of this tool is presented using Fructose to 5-Hydroxymethylfurfural as a case study.