SEML: A Simplified English Modeling Language for Constructing Biological Models in Julia

Abstract

Many markup languages can be used to encode biological networks, each with strengths and weaknesses. Model specifications written in these languages can then used, in conjunction with proprietary software packages e.g., MATLAB, or open community alternatives, to simulate the behavior of biological systems. In this study, we present the Simplified English Modeling Language (SEML) and associated compiler, as an alternative to existing approaches. SEML supports the specification of biological reaction systems in a simple natural language like syntax. Models encoded in SEML are transformed into executable code using a compiler written in the open-source Julia programming language. The compiler performs a sequence of operations, including tokenization, syntactic and semantic error checking, to convert SEML into an intermediate representation (IR). From the intermediate representation, the compiler then generates executable code in one of three programming languages: Julia, Python or MATLAB. Currently, SEML supports both kinetic and constraint based model generation for signal transduction and metabolic modeling. In this study, we demonstrate SEML by modeling two proof-of-concept prototypical networks: a constraint-based model solved using flux balance analysis (FBA) and a kinetic model encoded as Ordinary Differential Equations (ODEs). SEML is a promising tool for encoding and sharing human-readable biological models, however it is still in its infancy. With further development, SEML has the potential to handle more unstructured natural language inputs, generate more complex models types and convert its natural language markup to currently used model interchange formats such systems biology markup language.