A modelling portal for the UK plant systems biology community

英国植物系统生物学界的建模门户

• 批准号: BB/F010583/1
• 负责人: Andrew Millar
• 金额: $ 24.13万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FF010583%2F1
• 关键词: modelling; portal; UK; plant; systems

This project is all about plant growth models. Here, the word 'model' does not refer to a physical object but instead means a mathematical way of representing something. This kind of model consists of a series of mathematical equations which can be solved, normally using a computer. By feeding these equations with values for factors like temperature, amount of nitrogen available and light energy that plants can capture, the models make it possible to predict how a plant will grow. Many of the models available are for crop plants, and they can give estimates of how much a crop will produce, whether it is a wheat plant yielding grain, a tree growing new wood, or a pasture providing grass to feed animals. Some of the more complicated ones also represent interactions between plants and other species, such as bacteria and fungi which improve or reduce nutrient uptake by plant roots, or leaf-eating herbivores. Historically, these models work at the level of a whole plant, a farmer's field or even a landscape, because it has been most straightforward to collect data at these levels. Modelling plant growth, an area of research which has flourished for several decades, is one in which the UK has been especially strong, but which is not well known among modern molecular scientists. In the new era of 'systems biology' research, scientists are able to capture large amounts of data about processes that happen on a much finer scale - an individual leaf or root, for example, or even within a single cell. The challenge is to use this mass of information to predict how a plant's genetic makeup controls the way it grows and interacts with its environment. It is becoming clear that many of the mathematical techniques needed to make this possible are the same as those used by the crop modellers. The aim of the present project is to make existing crop models available to systems biology researchers via the Internet in a user-friendly way that is independent of any particular computer software. This means that systems biologists can adapt models for their own use, and connect them with other models that work at the cell level. We want to develop a portal, a one-stop Internet shop for the models themselves, examples of how they have been applied, and explanations detailed enough to allow other people to adopt them. We will also provide a forum so that the community can add comments and suggestions for further development, and help each other in using these and other models in the future. In addition to plant systems biology experts, the portal will be of use to crop scientists and to policy-makers. Predicted climate change will mean that our current crops will perform differently in the future - the models will help predict whether the difference will be beneficial or cause loss of yield or failure of crops. They will also aid researchers and breeders in developing crops for new uses, such as bioenergy. Some models have the capability to predict the behaviour of whole ecosystems, such as forests, under changing conditions. Models are important for the future of plant science research, agriculture and the environment and it is important to make them as widely accessible and usable as possible / this is the purpose of our project.

这个项目是关于植物生长模型的。在这里，“模型”这个词并不是指物理对象，而是指一种表示事物的数学方式。这种模型由一系列数学方程组成，通常可以使用计算机求解。通过为这些方程提供温度、可用氮量和植物可以捕获的光能等因素的值，这些模型可以预测植物将如何生长。许多可用的模型都是针对作物的，它们可以估算出一种作物的产量，无论它是一种生产谷物的小麦，一棵长出新木材的树，还是一片提供牧草喂养动物的牧场。一些更复杂的也代表了植物和其他物种之间的相互作用，例如细菌和真菌，它们可以提高或减少植物根部或食叶草食动物对养分的吸收。从历史上看，这些模型适用于整个工厂，农民的田地甚至景观的水平，因为在这些水平上收集数据是最直接的。模拟植物生长是一个蓬勃发展了几十年的研究领域，英国在这一领域尤其强大，但在现代分子科学家中并不为人所知。在“系统生物学”研究的新时代，科学家们能够捕获大量关于在更精细的尺度上发生的过程的数据-例如，单个叶子或根，甚至在单个细胞内。挑战在于利用这些大量的信息来预测植物的基因组成如何控制其生长方式以及与环境的相互作用。越来越清楚的是，使这成为可能所需的许多数学技术与作物建模者所使用的技术相同。本项目的目的是使系统生物学研究人员能够通过互联网以用户友好的方式获得现有的作物模型，而不依赖于任何特定的计算机软件。这意味着系统生物学家可以调整模型供自己使用，并将它们与在细胞水平上工作的其他模型连接起来。我们希望开发一个门户网站，一个一站式的互联网商店，为模型本身，他们如何被应用的例子，并解释详细到足以让其他人采用它们。我们还将提供一个论坛，以便社区可以为进一步开发添加评论和建议，并在未来使用这些和其他模型时相互帮助。除了植物系统生物学专家外，该门户网站还将对作物科学家和政策制定者有用。预测的气候变化将意味着我们目前的作物在未来的表现将有所不同-这些模型将有助于预测这种差异是有益的还是导致作物减产或歉收。它们还将帮助研究人员和育种者开发用于生物能源等新用途的作物。有些模型有能力预测整个生态系统，如森林在不断变化的条件下的行为。模型对于植物科学研究、农业和环境的未来是重要的，重要的是使它们尽可能广泛地可访问和可用/这是我们项目的目的。

项目成果

PlaSMo: Making existing plant and crop mathematical models available to plant systems biologists

PlaSMo：为植物系统生物学家提供现有的植物和作物数学模型

• DOI: 10.1016/j.cbpa.2009.04.562
• 发表时间: 2009
• 期刊: Molecular & Integrative Physiology
• 作者: Davey C

Development of a web portal for plant models

开发植物模型门户网站

• 发表时间: 2009
• 期刊: Journal of Agricultural Science
• 影响因子: 2
• 作者: Muetzelfeldt, R

Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT

温度通过整株FT积累影响开花的机制模型

• DOI: 10.1101/267104
• 发表时间: 2018
• 作者: Kinmonth-Schultz H

The grant is dead, long live the data - migration as a pragmatic exit strategy for research data preservation

拨款已死，数据万岁 - 迁移作为研究数据保存的务实退出策略

• DOI: 10.12688/wellcomeopenres.15341.1
• 发表时间: 2019
• 期刊: Wellcome Open Research
• 作者: Zielinski T