Building a Bioinformatics Ecosystem for Agri-Ecologists

组学时代预示着生物科学的兴奋。组学方法允许表型在基因组水平上被询问-基因组，转录组，表观基因组和蛋白质组。这些见解正在彻底改变生物科学的各个方面，包括农业和粮食生产：例如，基因及其调控机制可以被识别、编辑和改造，以选择农业生产的、抗病的表型，并控制害虫种群。但是，如果不了解围绕、支持和挑战农业系统的基本生物学，我们就无法将农业粮食系统转变为环境可持续和生产力足以养活地球变暖中不断增长的人口；例如，我们需要有效的方法来监测和检测病原体，评估集约化农业对传粉媒介和天然生物防治剂健康的影响。BBSRC认识到这一点，也认识到农业生态学家在缓解这些挑战方面发挥的关键作用。然而，这个群体正面临着落入组学缺口的风险，而且由于农业生态学家的生产力与他们分析数据所需的生物信息学技能和资源不匹配，他们的潜力被削弱了。我们的项目提供了支持该社区所需的资源，使英国农业生态学家能够直接解决BBSRC的战略目标，即提供可持续农业和粮食安全。我们将在世界领先的开放获取生物信息学工作流管理器Nextflow中实现用户友好的生物信息学管道，Nextflow提供直观的，无缝的“即插即用”模块化平台，提供管道来分析从序列数据到结果输出的数据，而无需能够编写或排除编码故障或处理包之间的不兼容性。工作流由模块组成，可以很容易地更新、切换、添加和删除，使有机的、响应的管道随着用户社区的增长而增长。有机的，经得起时间考验的特性是由超过10,000名成员（“非核心”）的开源社区的技能所实现的，他们共同测试，纠正，更新和完善管道。这种社区主导的方法意味着管道仍然是最先进的，可复制的，并得到来自学术界和工业界的生物信息学家的认可；由于管道是开源的，并且被广泛使用，这些资源在拨款期限之外是经得起未来考验的。我们将通过三个目标来实现这一目标：(1)建立一个农业生态学家社区，作为经济学大使；(2)提供满足生态群落需求的生物信息学管道；(3)向最终用户更广泛地传播管道；培训和激励创新。

The omics era heralds excitement for the biosciences. Omics approaches allow the phenotype to be interrogated at the genomic level - the genome, transcriptome, epigenome and proteome. Such insights are revolutionising all aspects of the biosciences, including agriculture and food production: for example, genes and their regulatory machinery can be identified, edited and engineered to select productive, disease-resistant phenotypes for farming and to control pest populations. But we cannot transform agri-food systems to be environmentally sustainable and productive enough to feed for our growing populations in a warming planet, without an understanding of the fundamental biology surrounding, supporting, and challenging agricultural systems; e.g. we need effective methods to monitor and detect pathogens, to assess the effects of intensive agriculture on the health of pollinators and natural biocontrol agents. The BBSRC recognises this and the critical role that agri-ecologists play in mitigating these challenges. Yet, this community is at risk of falling through the omics gap, and their potential curtailed due to mismatch in the productivity of agri-ecologists and the bioinformatics skills and resources they need to analyse their data. Our Project provides the resources needed to support this community, such that UK agri-ecologists are able to directly address the BBSRC's strategic goal to deliver sustainable agriculture and food security. We will implement user-friendly bioinformatics pipelines within the world-leading open-access bioinformatics workflow manager, Nextflow, which provides intuitive, seemless 'plug-and-play' modular platforms, delivering pipelines to analyse data from sequence data to results outputs without the need to be able to write or troubleshoot coding or deal with incompatibilities between packages. Workflows consist of modules, which can be easily updated, switched, added and removed, making organic, responsive pipelines that grow with the user community. The organic, time-proofed nature is made uniquely possible by the skills of an open-source community of over 10,000 members ('nf-core'), who collectively test, correct, update and refine pipelines. This community-led approach means that the pipelines remain state-of-the-art, reproducible, endorsed by bioinformaticians drawn from academia and industry; because pipelines are open-source and widely used, these resources are future-proofed beyond the life of the grant. We will achieve this through three Objectives: (1) Develop a community of agri-ecologist as Ambassadors for omics; (2) Deliver the bioinformatics pipelines needed to address the needs of the ecological community; (3) Wider dissemination of pipelines to end-users; train and stimulate innovation.