Kohl Michael
Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
Methods Mol Biol. 2011;696:413-27. doi: 10.1007/978-1-60761-987-1_26.
Modeling is a means for integrating the results from Genomics, Transcriptomics, Proteomics, and Metabolomics experiments and for gaining insights into the interaction of the constituents of biological systems. However, sharing such large amounts of frequently heterogeneous and distributed experimental data needs both standard data formats and public repositories. Standardization and a public storage system are also important for modeling due to the possibility of sharing models irrespective of the used software tools. Furthermore, rapid model development strongly benefits from available software packages that relieve the modeler of recurring tasks like numerical integration of rate equations or parameter estimation. In this chapter, the most common standard formats used for model encoding and some of the major public databases in this scientific field are presented. The main features of currently available modeling software are discussed and proposals for the application of such tools are given.
建模是一种整合基因组学、转录组学、蛋白质组学和代谢组学实验结果，并深入了解生物系统组成成分之间相互作用的手段。然而，共享如此大量的、通常是异构且分布式的实验数据既需要标准数据格式，也需要公共存储库。由于可以不考虑所使用的软件工具而共享模型，因此标准化和公共存储系统对于建模也很重要。此外，快速的模型开发极大地受益于可用的软件包，这些软件包可以减轻建模人员处理诸如速率方程的数值积分或参数估计等重复性任务的负担。在本章中，将介绍用于模型编码的最常见标准格式以及该科学领域中的一些主要公共数据库。还将讨论当前可用建模软件的主要特点，并给出应用此类工具的建议。
