BioPreDyn-bench

BioPreDyn-bench是一个专为系统生物学设计的基准数据集，包含六个不同的参数估计问题。这些问题涵盖了从细菌到动物细胞的多种生物系统，包括代谢、转录、信号转导和发育过程。数据集中的模型规模从中等到大规模，参数数量从数十到数千不等。每个问题都提供了详细的模型描述、实验数据、成本函数和参数范围，以及在Matlab和COPASI中的实现。这些基准问题不仅用于评估参数估计方法，还可用于敏感性和可识别性分析、模型简化及实验设计优化。

BioPreDyn-bench is a benchmark dataset specifically designed for systems biology, which comprises six distinct parameter estimation problems. These problems cover a wide range of biological systems ranging from bacteria to animal cells, including metabolic, transcriptional, signal transduction, and developmental processes. The models in the dataset range from medium-scale to large-scale, with the number of parameters varying from tens to thousands. Each problem provides detailed model descriptions, experimental data, cost functions, parameter ranges, as well as implementations in both Matlab and COPASI. These benchmark problems can be used not only for evaluating parameter estimation methods, but also for sensitivity and identifiability analysis, model reduction, and experimental design optimization.