Standardising the quality of genome scale models

AIMMS researchers contributed to the development of quality control tools for systems biology models in Nature Biotechnology

04/06/2020 | 2:11 PM

Moritz Bieber, Christian Lieven (Biosustain, DTU), Brett Olivier and Bas Teusink (AIMMS, VU Amsterdam) and a worldwide community of scientists developed quality control tools for systems biology models in Nature Biotechnology.
 
Mathematical models are a key tool to understand complex biological systems. In particular, constraint-based, genome scale, models (GSM's) can relate the physiological property of a cells, such as growth and metabolism, to the chemical flows through the underlying metabolic reaction network encoded by the genes. However, each model can in itself contain thousands of components. Moreover there is a continuous increase in number of these models being produced, using various semi-automated methods. The question arises, how do you evaluate a model's quality? Being able to answer this question is critical to a model’s reproducibility and reusability.
   
In a recent correspondence published in Nature Biotechnology Moritz Bieber, Christian Lieven (Biosustain, DTU) and a large, worldwide community of scientists including Brett Olivier and Bas Teusink (AIMMS, VU Amsterdam) set out to address this problem. The tool presented in this contribution, MEMOTE, leverages the advantages of the latest community developed model encoding standards (SBML FBC), and implements a pipeline containing a set of tests that evaluates a model's annotation, basic functionality and conceptual integrity. Hopefully, this will lead to a more efficient (re)use of genome-scale models in research and biotechnology. You can find the article in Nature Biotechnology here.