Related Experiment Video
Updated: Apr 15, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language
Nicholas Roehner1, Zhen Zhang2, Tramy Nguyen2
1†Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, United States.
Abstract:
In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).
Related Concept Videos
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Molecular Models
Mechanistic Models: Compartment Models in Individual and Population Analysis
Mechanistic Models: Overview of Compartment Models
Simplified Synchronous Machine Model
In this model, each generator is connected to a...
Mathematical Modeling: Problem Solving

