Modeling of gene regulatory networks: an annotated glossary

Biological processes are complex. Their behavior cannot be understood from the sum of their parts. Modeling, which allows for articulating hypotheses as equations and rules, has become indispensable for studying biological complexities. When written as computer code, mathematical models can be evaluated to test multiple potential outcomes. Modeling is useful for identifying essential system components and revealing new interactions. However, implementing models in biological research requires a solid understanding of computational and mathematical vocabulary, which typically requires formal training. Furthermore, communication barriers often hinder collaborations with computational modelers. To address this, we present an annotated glossary of terms associated with modeling gene regulatory networks. Aimed at biologists, we explain common computational modeling terms and frameworks using examples from published studies.