STFC/NERC Bioinformatics & Environmental 'Omics Network

基因组学革命的广泛影响已经触及生物学的各个方面。由于分子研究的新技术，基因组的组成和存在于基因组和生物体对环境的反应之间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），现在可以对它们进行完整的研究。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，而且还在环境生物学中创造了前所未有的信息学挑战。随着仪器技术的进步，组学研究产生的数据量比环境生物学中的标准数据量高出几个数量级，这给数据存储、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以为解决关键问题的创新提供重要的新机会。为了充分利用这些发展的潜力来实现其“下一代地球科学”战略，NERC建立了一个虚拟的环境组学合成中心，以促进环境组学的新科学方法的合并和出现。EOS的任务是使NERC社区能够出现新的科学合成，这些合成可能从环境组学中受益，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大规模复杂数据。因此，在NERC和STFC的现有设施基地所确定的对环境组学的生物信息学方法的扩大规模的新需求之间存在巨大的协同作用潜力，从而使双方受益。目前的STFC全球网络呼吁为STFC和NERC在环境科学方面的利益之间发展强有力的联系提供了及时的机会。事实上，第二届STFC环境未来研讨会（http://www.stfc.ac.uk/resources/pdf/FuturesEnv2Report.pdf）特别强调了环境组学带来的生物信息学挑战。NERC EOS刚刚建立，因此在这个阶段与STFC科学家建立的网络将确保STFC广泛的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得到发展。我们计划每年举办两次研讨会，在每个案例中讨论STFC和NERC之间预期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)新颖的数据结构，新颖的算法和本体。环境组学提出的生物信息学挑战得到了广泛的认可，但是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，例如涉及气候和其他主要环境循环的数据结构和模型。(c)环境生物过程与人类健康之间的相互作用，例如作为威胁健康的抗菌素耐药性来源的环境毒理学和环境污染。d)模拟基本生态系统服务及其对环境变化的适应能力背后的复杂生物相互作用。

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.