Villaverde Alejandro F, Henriques David, Smallbone Kieran, Bongard Sophia, Schmid Joachim, Cicin-Sain Damjan, Crombach Anton, Saez-Rodriguez Julio, Mauch Klaus, Balsa-Canto Eva, Mendes Pedro, Jaeger Johannes, Banga Julio R
Bioprocess Engineering Group, IIM-CSIC, Eduardo Cabello 6, Vigo, 36208, Spain.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK.
BMC Syst Biol. 2015 Feb 20;9:8. doi: 10.1186/s12918-015-0144-4.
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The community has already developed many methods and software packages which aim to facilitate these tasks. However, there is a lack of suitable benchmark problems which allow a fair and systematic evaluation and comparison of these contributions.
Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area. This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli, baker's yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The level of description includes metabolism, transcription, signal transduction, and development. For each problem we provide (i) a basic description and formulation, (ii) implementations ready-to-run in several formats, (iii) computational results obtained with specific solvers, (iv) a basic analysis and interpretation.
This suite of benchmark problems can be readily used to evaluate and compare parameter estimation methods. Further, it can also be used to build test problems for sensitivity and identifiability analysis, model reduction and optimal experimental design methods. The suite, including codes and documentation, can be freely downloaded from the BioPreDyn-bench website, https://sites.google.com/site/biopredynbenchmarks/ .
动态建模是系统生物学的基石之一。目前，许多研究工作都投入到了大规模动力学模型的开发和应用中。参数估计（模型校准）和最优实验设计等相关问题极具挑战性。该领域已经开发出了许多旨在促进这些任务的方法和软件包。然而，缺乏合适的基准问题来对这些成果进行公平、系统的评估和比较。
在此，我们展示了BioPreDyn-bench，这是一组具有挑战性的参数估计问题，旨在作为该领域的参考测试案例。该集合包含六个问题，涵盖了大肠杆菌、酿酒酵母、黑腹果蝇、中国仓鼠卵巢细胞的中大型动力学模型，以及一个通用信号转导网络。描述层面包括代谢、转录、信号转导和发育。对于每个问题，我们提供：（i）基本描述和公式；（ii）多种格式的可直接运行的实现；（iii）使用特定求解器获得的计算结果；（iv）基本分析和解释。
这套基准问题可随时用于评估和比较参数估计方法。此外，它还可用于构建敏感性和可识别性分析、模型简化和最优实验设计方法的测试问题。该套件，包括代码和文档，可从BioPreDyn-bench网站（https://sites.google.com/site/biopredynbenchmarks/ ）免费下载。
