Building a Bioinformatics Ecosystem for Agri-Ecologists

组学时代预示着生物科学的兴奋。组学方法允许在基因组水平-基因组、转录组、表观基因组和蛋白质组-上询问表型。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，编辑和工程化，以选择生产，抗病的农业表型和控制害虫种群。但是，如果我们不了解农业系统周围的基本生物学，支持和挑战农业系统，我们就无法将农业食品系统转变为环境可持续性和生产力足以养活我们在变暖的星球上不断增长的人口;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者和天然生物控制剂健康的影响。BBSRC认识到这一点以及农业生态学家在缓解这些挑战方面发挥的关键作用。然而，这个社区有可能陷入组学差距，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，他们的潜力受到限制。我们的项目提供了支持这个社区所需的资源，使英国农业生态学家能够直接解决BBSRC的战略目标，以实现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中实施用户友好的生物信息学管道，Nextflow提供直观，无障碍的“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，而无需编写或解决编码问题或处理包之间的不兼容性。工作流由模块组成，可以轻松地更新，切换，添加和删除，使有机，响应管道与用户社区一起增长。有机的，不受时间限制的性质是由超过10，000名成员（'nf-core'）的开源社区的技能所独有的，他们共同测试，纠正，更新和完善管道。这种以社区为主导的方法意味着管道仍然是最先进的，可复制的，由来自学术界和工业界的生物信息学家认可;因为管道是开源的，广泛使用的，这些资源在赠款的生命周期之外是面向未来的。我们将通过三个目标来实现这一目标：（1）发展一个农业生态学家社区作为组学大使;（2）提供满足生态社区需求所需的生物信息学管道;（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.