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.

中文翻译：

---

评估不同酵母物种基因组规模代谢模型的可访问性、可用性和互操作性

代谢网络重建已成为系统生物学领域探索细胞代谢的重要工具。它们被用作定量预测的工具，也被用作进一步知识情境化的支架。酿酒酵母是最早于 2003 年重建基因组规模代谢模型 (GEM) 的生物体之一，此后已为各种相关酵母物种开发了 45 个代谢模型。对这些模型的系统评估表明，尽管建模历史很长，但跟踪模型文件、为基本模拟目的设置模型以及跨物种甚至不同版本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 可供更广泛的公众使用和使用。