Bridging systems biology and advanced computing, to realise multi-scale biological modelling.

生命科学正处于空前的扩张之中，以至于21世纪被称为“生物学的世纪”。该交换奖学金将从世界领先的计算科学中心——EPCC（由其高级软件架构师之一阿拉斯泰尔·休谟所代表）招募经验，以建立一个长期的合作伙伴关系，以维持英国计算机科学的发展美国在生物学前沿的优势。这种专业知识是迫切需要的，因为数学和计算建模是生命科学研究领域广泛和不断增长的下一个推动力。突破性的“全细胞”模型的发表（Karr et al., 2012）通过表示（非常简单的）细胞中每个基因的功能，激发了系统生物学领域的这项研究。这个里程碑式的多尺度建模桥梁从基因组到细胞功能。从细胞到器官和有机体水平的生理模型已经存在，不仅在开创性的哺乳动物心脏模型中，而且在作物科学的植物水平模型中。因此，“全细胞”模型是实现从基因型到表型或从基因组序列到临床特征联系的关键一步。植物模型甚至与田间规模以及通常有助于作物和气候预测的更大的农业和生态模型联系在一起。包括全细胞模型作者在内的许多人强调，生物学家必须与计算机科学家在数据管理、模型集成、加速计算和数据分析方面进行合作（Macklin et al.）。标准和软件必须不断发展以跟上步伐。工作范例模型对于指定下一代解决方案至关重要。SynthSys的研究人员正在使用“全细胞”范例模型，并为更复杂的细胞开发模型。SynthSys是由BBSRC和EPSRC建立的，是英国六个系统生物学中心之一，专注于细胞和分子生物学建模。安德鲁·米勒（Andrew Millar）的团队基于BBSRC的这一重大投资，开发了拟南芥生长的全植物框架模型。它不仅是为数不多的可用于指定未来计算基础设施的范例之一，而且还支持从基础系统生物学到作物科学的日益增长的联系。我们很荣幸能与Alastair Hume合作，他完美地满足了我们当前研究的迫切需求。Hume在工业界和学术界拥有超过20年的软件开发经验。在EPCC工作的14年里，他领导了从天文学到环境建模和预测等各种研究领域的可扩展数据集成、处理和分析系统的设计和实施。例如，在最近的欧盟BonFIRE项目中，他领导了一个由20名软件开发人员组成的团队，致力于未来的云计算。休谟已经在与SynthSys的联合试点项目中展示了他的潜力，现在他准备做出长期贡献。该奖学金对于实现跨学科转换至关重要，使他能够在系统生物学方面接受培训，包括在EBI实习，与更广泛的系统生物学建模社区接触，以及在三个领域解决示范项目。我们的多尺度模型明确旨在将来自不同科学背景的研究人员联系起来，他们必须共同提供数据，建模组件和验证实验。该奖学金将在英国和美国与我们在洛桑研究与仿真有限公司的合作伙伴进行这一重要的网络交流。该奖学金将使SynthSys和EPCC共同将我们的工作与计算资源和生物建模方面的国际领先者联系起来，为英国创造一个制高点在三个快速发展的领域：植物系统生物学、网络基础设施和多尺度作物建模之间的联系。

The life sciences are in the midst of an unparalleled expansion, so much that the 21st-century has been termed "the century of biology". This interchange Fellowship will recruit the experience from a world-leading centre for computational science, EPCC, personified by Alastair Hume one of its senior software architects, to build a long-term partnership that maintains the U.K.'s advantage at the forefront of Biology. Such expertise is urgently required, because mathematical and computational modelling is the next driver of progress for a broad and growing swathe of life science research. The publication of a ground-breaking "whole-cell" model (Karr et al., 2012) has galvanised this research in the field of Systems Biology, by representing the function of every gene in a (very simple) cell. This landmark in multi-scale modelling bridges from the genome to cell function. Physiological models already exist that span from cellular to organ and organism level, not only in the pioneering mammalian heart model but also in the plant-level models of crop science. Thus the "whole-cell" model is a crucial step towards a link from genotype to phenotype or from genome sequence to clinical traits. The plant models link even further, to the field scale and to larger agricultural and ecological models that routinely contribute to crop and climate forecasting.The whole-cell model's authors are among many to stress that biologists must collaborate with computer scientists in data curation, model integration, accelerated computation and data analysis (Macklin et al.). Standards and software must constantly evolve to keep pace. Working, exemplar models are essential to specify the next-generation solutions. Researchers at SynthSys are using the "whole-cell" exemplar model and developing models for more complex cells. SynthSys was established by BBSRC and EPSRC as one of six UK Systems Biology centres, to focus on modelling cell and molecular biology. Andrew Millar's group has developed a whole-plant Framework Model of Arabidopsis growth, building on this major BBSRC investment. It is not only one of the very few exemplars that can be used to specify future computational infrastructure, but is also supporting a growing link from fundamental Systems Biology to Crop Science.We are privileged to work with Alastair Hume, who ideally meets the urgent needs of our current research. Hume has over 20 years' experience in software development in industry and academia. While working at EPCC over the last 14 years, he has led the design and implementation of scalable data integration, processing and analysis systems for a variety of research fields ranging from astronomy to environmental modelling and prediction. In the recent EU BonFIRE project, for example, he led a team of up to 20 software developers working on future cloud computing.Hume has already demonstrated his potential in joint, pilot projects with SynthSys and he is now poised to make a long-term contribution. The Fellowship is essential to realise that interdisciplinary conversion, allowing him to train in systems biology including an internship at the EBI, to engage with the broader systems biology modelling community, as well as addressing demonstration projects in three areas. Our multiscale models explicitly aim to link researchers from different scientific backgrounds, who must work together to provide the data, the modelling components and validation experiments. The Fellowship will provide time for this crucial networking, in the UK and USA, and with our partners at Rothamsted Research and Simulistics Ltd. This Fellowship will allow SynthSys and EPCC jointly to link our work to international leaders in both computational resources and in biological modelling, creating a commanding position for the U.K.'s research and Alastair Hume in particular, at the nexus of three fast-moving areas: plant systems biology, cyber-infrastructure and multi-scale crop modelling.