STFC/NERC Bioinformatics & Environmental 'Omics Network

STFC/NERC 生物信息学

• 批准号: ST/K001760/1
• 负责人: Thomas Meagher
• 金额: $ 30.54万
• 依托单位: University of St Andrews
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=ST%2FK001760%2F1
• 关键词: STFC; NERC; Bioinformatics; Environmental; Omics

The widespread impact of the genomics revolution has reached into every aspect of biology. As a result of new technologies for molecular investigation, the composition of the genome and the various organisational layers that exist between the genome and organismic response to the environment are now better described. These organisational layers, known as 'omics (e.g., genomics, transcriptomics, proteomics, metabolomics, etc), are now accessible for investigation in their entirety. This scope of investigation has not only opened unparalleled opportunities for a more complete understanding of how organisms or communities interact with the environment but also created an informatics challenge unprecedented in environmental biology. With technical advances in instrumentation, the sheer volume of data generated by 'omics investigation is orders of magnitude higher that has been the norm in environmental biology, creating new challenges for data storage, data analysis, and indeed optimisation of data structures generally. At the same time, important new opportunities for innovation in addressing critical problems can arise from the effective blending of bioinformatics and environmental 'omics. To leverage the full potential of these developments to deliver its strategy, 'Next Generation Science for Planet Earth', the NERC has established a virtual Environmental 'Omics Synthesis Centre to facilitate the coalescence and emergence of novel scientific approaches to environmental 'omics. EOS is tasked with enabling the emergence of novel scientific synthesis within the NERC community that might benefit from environmental 'omics as well as contribute to its development. STFC has a well-established infrastructure for addressing complex data on the scale that is likely to be generated through future investigations in environmental 'omics. Therefore there is substantial potential for synergism between the emerging need for enhanced scale of bioinformatics approaches to environmental 'omics as indentified by the NERC and the existing facilities base in the STFC, to the benefit of both.The present STFC Global Networks call provides a timely opportunity for the development of strong connections between STFC and NERC interests in environmental sciences. Indeed, the bioinformatics challenge presented by environmental 'omics was specifically highlighted at the second STFC Environment Futures Workshop (http://www.stfc.ac.uk/resources/pdf/FuturesEnv2Report.pdf). The NERC EOS is just now being established, so that network building with STFC scientists at this stage will ensure that the extensive resource base of the STFC will be an integral part of bioinformatics and environmental 'omics as collaboration between these fields is developed over the next five years.We plan to conduct two workshops per year, addressing in each case targeted research areas where there is anticipated potential for synergy between STFC and NERC. At the outset, indicative workshop themes for exploring joint STFC and NERC development of the potential of bioinformatics and environmental 'omics include:a) Novel data structures, novel algorithms and ontologies. The bioinformatics challenges raised by environmental 'omics are widely recognised, but both the detailed nature of these challenges and effective approaches for addressing them require further development. b) Linking environmental 'omics to other large scale data structures and models, for example those involving climate and other major environmental cycles.c) The interplay between environmental biological processes and human health, for example environmental toxicology and environmental pollution as a source of health-threatening antimicrobial resistance.d) Modelling complex biological interactions underlying basic ecosystem services and their resilience to environmental change.

基因组学革命的广泛影响已触及生物学的各个方面。由于分子研究的新技术，基因组的组成以及基因组和器官对环境的反应之间存在的各种组织层现在得到了更好的描述。这些组织层，被称为“组学”（例如，基因组学、转录组学、蛋白质组学、代谢组学等），现在可用于整体研究。这种调查范围不仅为更全面地了解生物体或群落如何与环境相互作用提供了前所未有的机会，而且也为环境生物学带来了前所未有的信息学挑战。随着仪器的技术进步，组学研究产生的数据量比环境生物学中的标准高出几个数量级，为数据存储，数据分析以及数据结构的优化带来了新的挑战。与此同时，生物信息学和环境组学的有效结合可能为解决关键问题的创新带来重要的新机会。为了充分利用这些发展的潜力，以实现其战略，“下一代地球科学”，NERC建立了一个虚拟的环境“组学合成中心”，以促进环境“组学”新科学方法的融合和出现。EOS的任务是使NERC社区内出现新的科学综合，这些科学综合可能受益于环境组学并有助于其发展。STFC拥有完善的基础设施，可以处理未来环境组学调查可能产生的复杂数据。因此，NERC所确定的环境组学生物信息学方法的规模扩大的新需求与STFC现有的设施基础之间存在着巨大的协同作用潜力，这对双方都有利。目前STFC全球网络的呼吁为STFC和NERC在环境科学领域的利益之间建立强有力的联系提供了一个及时的机会。实际上，科技委第二次环境未来讲习班特别强调了环境组学提出的生物信息学挑战（http：//www.stfc.ac.uk/resources/pdf/FuturesEnv2Report.pdf）。NERC EOS目前正在建立中，因此在现阶段与STFC科学家建立网络将确保STFC的广泛资源基础将成为生物信息学和环境组学的一个组成部分，因为这些领域之间的合作将在未来五年内发展。我们计划每年举办两次研讨会，在每一种情况下，处理预期STFC和NERC之间有协同潜力的目标研究领域。首先，探讨STFC和NERC联合开发生物信息学和环境组学潜力的指示性研讨会主题包括：a）新的数据结构，新的算法和本体。环境组学提出的生物信息学挑战已得到广泛承认，但这些挑战的详细性质和解决这些挑战的有效方法都需要进一步发展。B）将环境组学与其他大规模数据结构和模型联系起来，例如那些涉及气候和其他主要环境周期的数据结构和模型。c）环境生物过程与人类健康之间的相互作用，例如环境毒理学和环境污染作为威胁健康的抗生素耐药性的来源。d）模拟基本生态系统服务及其对环境变化的适应能力所依据的复杂生物相互作用。

项目成果

UAVs in pursuit of plant conservation - Real world experiences

• DOI: 10.1016/j.ecoinf.2017.11.001
• 发表时间: 2017-11
• 期刊: Ecol. Informatics
• 作者: S. Baena;D. Boyd;J. Moat

UAV survey at archaeological earthwork sites in the Brazilian state of Acre, southwestern Amazonia

• DOI: 10.1002/arp.1747
• 发表时间: 2019-08
• 期刊: Archaeological Prospection
• 影响因子: 1.8
• 作者: Sanna Saunaluoma;Niko Anttiroiko;J. Moat