Cooper Jonathan, Vik Jon Olav, Waltemath Dagmar
Department of Computer Science, University of Oxford, Parks Road, Oxford OX1 3QD, UK.
Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
Prog Biophys Mol Biol. 2015 Jan;117(1):99-106. doi: 10.1016/j.pbiomolbio.2014.10.001. Epub 2014 Nov 26.
Experimentation is fundamental to the scientific method, whether for exploration, description or explanation. We argue that promoting the reuse of virtual experiments (the in silico analogues of wet-lab or field experiments) would vastly improve the usefulness and relevance of computational models, encouraging critical scrutiny of models and serving as a common language between modellers and experimentalists. We review the benefits of reusable virtual experiments: in specifying, assaying, and comparing the behavioural repertoires of models; as prerequisites for reproducible research; to guide model reuse and composition; and for quality assurance in the translational application of models. A key step towards achieving this is that models and experimental protocols should be represented separately, but annotated so as to facilitate the linking of models to experiments and data. Lastly, we outline how the rigorous, streamlined confrontation between experimental datasets and candidate models would enable a "continuous integration" of biological knowledge, transforming our approach to systems biology.
实验是科学方法的基础,无论是用于探索、描述还是解释。我们认为,促进虚拟实验(湿实验室或实地实验的计算机模拟)的重用将极大地提高计算模型的实用性和相关性,鼓励对模型进行批判性审查,并成为建模者和实验者之间的通用语言。我们回顾了可重用虚拟实验的好处:在指定、分析和比较模型的行为库方面;作为可重复研究的先决条件;指导模型重用和组合;以及在模型的转化应用中进行质量保证。实现这一目标的关键一步是,模型和实验方案应分别表示,但要进行注释,以便于将模型与实验和数据联系起来。最后,我们概述了实验数据集与候选模型之间严格、简化的对比将如何实现生物学知识的“持续整合”,从而改变我们处理系统生物学的方法。