BioModels Database: a Unified resource for Systems Biology models

即使是最简单的生物体也会执行大量不同的过程，这些过程以复杂的方式相互联系，以确保有机体对环境做出适当的反应。确保我们真正了解这些过程是如何结合在一起的方法之一是建立它们的量化模型，可以用计算机模拟。如果计算机模拟的行为与真实生物体的行为不同，我们就知道我们忽略了系统的一个重要组成部分。定量模型还可以揭示复杂系统以前不为人知的特性，例如为新的药物治疗铺平道路。这种被称为计算系统生物学的方法正变得越来越受欢迎，因为科学家们正在积累许多生物体的详细部件清单，这要归功于全面记录生命实体组成的“组学”努力。Biomodels数据库提供了对生化和细胞生物系统的定量模型的访问，这些模型已经发表在科学文献中，并被证实是准确的。其中一些模型非常简单，只包含几个过程或反应；另一些包含数百个。检查模型以验证它们的行为是否如参考出版物中所述。人工策展人对模型的组件进行注释并将其交叉链接到其他相关数据资源。这使用户能够准确地识别模型的组件，并帮助他们检索适当的模型，然后他们可以使用适当的软件可视化和模拟。例如，为了开发细胞肿瘤发生的定量模型，人们可以选择合适的细胞周期模型，并尝试将其与相关细胞信号通路的模型合并，如MAP激酶级联。只有可信的、同行评议的、带注释的模型数据库才能提供足够的选择来建造砖块。用户可以根据许多不同的标准搜索模型，可视化并下载各种标准格式的模型以供进一步使用。在过去的两年里，Biomodels数据库经历了指数级的增长。它现在是定量模型的参考数据来源。几种科学期刊建议在发表时沉积模型，该数据库已被一项独立的社区调查评为系统生物学中使用最多的数据资源。作为概念验证而开发的Biomodels数据库已经证明了它的相关性，需要在更成熟的资源中发展，以便最好地服务于不断增长的英国系统生物学社区的需求。

Even the simplest living organisms perform a huge number of different processes, which are interconnected in complex ways to ensure that the organism responds appropriately to its environment. One of the ways of ensuring that we really understand how these processes fit together is to build quantitative models of them, that can be simulated using computer. If a computer simulation behaves differently than the real organism, we know that we've neglected an important component of the system. Quantitative models can also reveal previously unappreciated properties of complex systems, for instance paving the way toward new drug treatments. This approach, known as 'Computational Systems Biology', is becoming increasingly popular now that scientists are accumulating detailed parts lists for many organisms, thanks to the 'omics' efforts to comprehensively document the components of living entities. BioModels Database provides access to quantitative models of biochemical and cell biological systems that have been published in the scientific literature, and verified to be accurate. Some of these models are very simple, containing just a few processes or reactions; others contain hundreds. The models are checked to verify that they behave as described in the reference publication. Human curators annotate and cross link components of the models to other relevant data resources. This allows users to identify precisely the components of models, and helps them to retrieve appropriate models, which they can then visualise and simulate using appropriate software. For instance, in order to develop a quantitative model of cell tumorigenesis, one may choose a suitable model of cell-cycle, and attempt to merge it with models of relevant cell signalling pathways such as the MAP kinase cascade. Only a database of trusted, peer-reviewed, annotated models will provide the adequate choice of 'building bricks'. Users can search models on many different criteria, visualise and and download them in various standard formats for further use. Over the last two years, BioModels Database has undergone an exponential growth. It is now the reference data resource for quantitative models. Deposition of models upon publication is advised by several scientific journals, and the atabase has been voted most used data resource in Systems Biology by an independent community survey. Developed as a proof of concept, BioModels Database has demonstrated its relevance and needs to evolve in a more mature resource in order to best serve the need of a growing UK Systems Biology community.