biological models

A standard-enabled workflow for synthetic biology

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select …

Toward Community Standards and Software for Whole-Cell Modeling

Objective: Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells. Methods: We organized the 2015 Whole-Cell …

Synthetic Biology Open Language (SBOL) Version 2.0.0

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long …

Production-passage-time approximation: a new approximation method to accelerate the simulation process of enzymatic reactions

Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This paper introduces a new approximation method to reduce the computational cost of …