BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
复制标题
DOI：
10.1186/s12918-015-0144-4
复制
发表时间：
2015-02-20
影响因子：
--
通讯作者：
Banga JR
中科院分区：
文献类型：
--
作者：
Villaverde AF;Henriques D;Smallbone K;Bongard S;Schmid J;Cicin-Sain D;Crombach A;Saez-Rodriguez J;Mauch K;Balsa-Canto E;Mendes P;Jaeger J;Banga JR
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大规模动力学模型的开发和利用中。参数估计（模型校准）和最优实验设计的相关问题是特别具有挑战性的。社区已经开发了许多方法和软件包，旨在促进这些任务。然而，缺乏适当的基准问题，无法对这些贡献进行公平和系统的评价和比较。在这里，我们提出了BioPreDyn-bench，一组具有挑战性的参数估计问题，渴望在这一领域作为参考测试案例。这一套包括六个问题，包括中型和大型的动力学模型的细菌E。coli、面包酵母S. cerevisiae、醋蝇D.黑腹果蝇、中国果蝇卵巢细胞和一个通用的信号转导网络。描述的层次包括代谢、转录、信号转导和发育。对于每个问题，我们提供（i）一个基本的描述和制定，（ii）实现准备运行在几种格式，（iii）计算结果与特定的求解器，（iv）一个基本的分析和解释。这套基准问题可以很容易地用来评估和比较参数估计方法。此外，它也可以用来建立测试问题的灵敏度和可识别性分析，模型降阶和最优实验设计方法。该套件，包括代码和文档，可以从BioPreDyn-bench网站https://sites.google.com/site/biopredynbenchmarks/免费下载。本文的在线版本（doi：10.1186/s12918-015-0144-4）包含补充材料，可供授权用户使用。
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/. The online version of this article (doi:10.1186/s12918-015-0144-4) contains supplementary material, which is available to authorized users.
登录
查看更多内容
DOI：
10.1196/annals.1407.006
发表时间：
2007-01-01
期刊：
REVERSE ENGINEERING BIOLOGICAL NETWORKS
影响因子：
--
作者：
Camacho, Diogo;Licona, Paola Vera;Laubenbacher, Reinhard
通讯作者：
Laubenbacher, Reinhard
影响因子：
4.3
作者：
Crombach A;Wotton KR;Cicin-Sain D;Ashyraliyev M;Jaeger J
通讯作者：
Jaeger J
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
5.4
作者：
Cedersund, Gunnar
通讯作者：
Cedersund, Gunnar
影响因子：
--
作者：
Heavner BD;Smallbone K;Barker B;Mendes P;Walker LP
通讯作者：
Walker LP