BBR GenomeHubs - agile genome databasing for neglected organisms of agricultural, development and biodiversity importance

构建人类基因组的第一个草图花费了大约25亿英镑。新的测序技术意味着重新测序人类的成本降低了一百万倍以上。这种成本的降低也改变了基因组学方法来解决许多其他生物学问题。基因组学现在普遍应用于从作物和牲畜改良、病原体和寄生虫监测到生物多样性评估的各种目标。许多研究团体现在能够为他们的目标物种生成参考基因组，比较相关物种的基因组，并对同一物种的许多个体进行测序，以研究基因组序列之间的差异如何影响生物学。这些好处带来了管理大量数据的挑战，分析数据以回答问题，并将数据和结果提供给他人。对于原始序列数据，标准的做法是将其存放在“记录数据库”（收集、整理和存储以供后代使用的国际支持系统）中。然而，许多发现都是基于深入分析的数据-原始序列被“组装”以预测整个基因组序列，基因在该基因组序列中被预测，并且它们的功能通过一系列注释工具推断。强烈鼓励在记录数据库中记录这些分析，但在技术上有困难。对于少数物种，研究人员已经开发出专门的基因组探索数据库，不仅收集和整理序列，还收集和整理注释和功能数据，并以促进整合的方式呈现。这些数据库需要大量的专业知识和努力来建立、维护和跟上最新的科学发展。因此，对于大多数物种，特别是发展中国家感兴趣的物种，不存在专门的数据库，社区缺乏资源来填补这一空白。在以前的BBR项目中，我们开发了一种基因组数据库的方法，称为GenomeHubs，它消除了为任何物种组创建和维护专用基因组学资源的障碍。我们通过极大地简化将数据导入最全面的基因组数据库平台Ensembl并托管其实例的过程来做到这一点。使用精心设计的Ensembl系统，我们开发了一些工具，这些工具可以收集来自不同来源的数据，运行自动化分析，将分析结果导入数据库，并通过Web界面可视化基因组和注释。在这项提案中，我们将进一步开发GenomeHubs，使研究人员能够直接运行所有步骤，对任何基因组或基因组组进行组装、注释和标准分析，并与更广泛的社区分享这些结果。我们将增加新的分析和可视化，我们将通过合作和培训帮助用户设置和使用GenomeHubs。该应用程序正在与BBSRC BBR全球挑战研究资助电话一起进行，该电话将与中低收入国家（LMIC）的科学家合作开发和利用GenomeHubs以满足他们的需求。基因组学正越来越多地应用于解决发展中国家的问题，特别是作物和当地农场动物的改良，了解和防治传染病，以及生物多样性保护。该项目将与GCRF GenomeHubs外展项目密切合作，将该技术带给LMIC研究人员并支持他们使用GenomeHubs。我们将把研究界联系起来，促进数据共享，加强资源的汇集和理解，以解决共同的问题。我们将与LMIC的主要科学家合作，他们将担任GenomeHubs的大使，并与LMIC的研究人员密切合作，为GenomeHubs开发新的代码，新的可视化和新的分析工具，以满足他们的要求。

Building the first draft of the human genome cost around £2.5 billion. New sequencing technologies mean the cost of resequencing a human has reduced over a million-fold. This reduction in cost also transforms genomics approaches to many other biological questions. Genomics is now commonly applied to diverse goals from crop and livestock improvement, through pathogen and parasite surveillance, to biodiversity assessment. Many research communities are now able to generate reference genomes for their target species, compare genomes across suites of related species and sequence many individuals of the same species to investigate how variation between genome sequences affects biology.With these benefits come the challenges of managing a deluge of data, of analysing the data to answer questions, and of making the data and results available to others. For raw sequence data deposition in "databases of record" (internationally-supported systems that collect, collate and store for posterity) is standard. However, many discoveries are based on intensively analysed data - raw sequence is "assembled" to predict the whole genome sequence, genes are predicted in this genome sequence, and their functions are inferred by a range of annotation tools. Capturing these analyses in databases of record is strongly encouraged, but is technically difficult. For a few species, researchers have developed dedicated genome exploration databases that collect and collate not only sequence but also annotation and functional data, and present it in a way that facilitates integration. These databases require considerable expertise and effort to set up, maintain and keep current with the latest scientific developments. Thus, for the majority of species, and especially species of interest to the developing world, dedicated databases do not exist and communities lack the resources to plug this gap.During a previous BBR project, we developed an approach to genome databasing, named GenomeHubs, that removes the barriers to creating and maintaining a dedicated genomics resource for any species group. We do this by greatly simplifying the process of importing data into, and hosting an instance of, the most comprehensive genome database platform, Ensembl. Using the carefully-engineered Ensembl system, we have developed tools that standardise data from diverse sources, run automated analyses, import analysis results back into the database and visualise the genome and annotations through a web interface. In this proposal we will develop GenomeHubs further to make it straightforward for researchers to run all the steps to assemble, annotate and run standard analyses on any genome or set of genomes and share these results with the wider community. We will add new analyses and visualisations and we will help users through collaboration and training in the setup and use of GenomeHubs.This application is being made in tandem with one to the BBSRC BBR Global Challenges Research Funding call, which will work with Lower and Middle Income Country (LMIC) scientists to develop and exploit GenomeHubs for their needs. Genomics is being increasingly applied to problems of the developing world, in particular improvement of crop plants and local farm animals, understanding and combating infectious disease, and biodiversity conservation. This project will work very closely with the GCRF GenomeHubs outreach project, bringing the technology to LMIC researchers and supporting their use of GenomeHubs. We will link research communities, promote data sharing and enhance the pooling of resources and understanding to solve shared problems. We will develop collaborations with key scientists in LMICs who will act as Ambassadors for GenomeHubs, and collaborate closely with LMIC researchers to develop new code, new visualisations and new analytic tools for GenomeHubs to meet their requirements.