Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden.
FEMS Yeast Res. 2021 Mar 4;21(1). doi: 10.1093/femsyr/foab002.
Metabolic network reconstructions have become an important tool for probing cellular metabolism in the field of systems biology. They are used as tools for quantitative prediction but also as scaffolds for further knowledge contextualization. The yeast Saccharomyces cerevisiae was one of the first organisms for which a genome-scale metabolic model (GEM) was reconstructed, in 2003, and since then 45 metabolic models have been developed for a wide variety of relevant yeasts species. A systematic evaluation of these models revealed that-despite this long modeling history-the sequential process of tracing model files, setting them up for basic simulation purposes and comparing them across species and even different versions, is still not a generalizable task. These findings call the yeast modeling community to comply to standard practices on model development and sharing in order to make GEMs accessible and useful for a wider public.
代谢网络重建已成为系统生物学领域探究细胞代谢的重要工具。它们不仅可用作定量预测的工具，还可用作进一步知识情境化的支架。酵母酿酒酵母是最早构建基因组尺度代谢模型 (GEM) 的生物体之一，该模型于 2003 年构建，此后，已经为多种相关酵母物种开发了 45 种代谢模型。对这些模型的系统评估表明，尽管有如此长的建模历史，但跟踪模型文件、为基本模拟目的设置模型以及在物种之间甚至不同版本之间进行比较的顺序过程仍然不是一项可推广的任务。这些发现呼吁酵母建模界遵守模型开发和共享的标准实践，以使 GEM 更容易为更广泛的公众所接受和使用。
