Tummler Katja, Klipp Edda
Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany.
FEMS Yeast Res. 2024 Jan 9;24. doi: 10.1093/femsyr/foae011.
Data makes the world go round-and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should-in its entirety-cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
数据推动世界运转，而高质量数据是精确模型的先决条件，尤其是对于全细胞模型（WCM）而言。WCM的数据必须可重复使用，包含有关确切实验背景的信息，并且应整体涵盖细胞中的所有相关过程。在此，我们回顾了WCM数据的基本要求以及将它们结合起来的策略。作为一种物种特异性资源，我们引入酵母细胞模型数据库（YCMDB）来说明要求和解决方案。我们讨论了数据以及计算模型的最新标准，包括作为要报告的数据的建模过程。尽管WCM具有内在复杂性，我们仍概述了构建WCM的策略。
