iPlant UK

随着新的高通量技术支持更快、更便宜的测序、代谢物和图像数据的产生，生物学日益成为一门“大数据”科学。这使得潜在的令人兴奋的突破成为可能，因为研究人员发现了未被发现的模式，并做出了具有生物学意义的新发现。然而，由于缺乏计算资源、适当的支持和技术技能，许多个体生物学家，在某些领域，甚至整个社区，都难以充分利用所产生的数据。它不仅是数据分析的输出，如模型、精选数据集或原始数据，对更广泛的社区具有价值，而且还包括在研究项目期间产生的工具，用于支持研究人员测试和验证他们的假设。目前，这些工具通常停留在原型形式，仅在生成它们的团队或实验室内使用，因为相对较少的标准化和共享工具的可访问、用户友好的版本的方法也不容易。因此，为了进行世界级的生物科学，研究人员需要能够存储和访问数据集、模型和分析工具，由于需要国际合作，最好是从全球不同的地点。IFactory Collaborative是由美国国家科学基金会(NSF)于2008年资助的，以帮助解决这些问题。IPLANT数据存储是一个基于云的存储空间，可通过iPLANT的发现环境(DE)进行访问，这是一个虚拟工作/实验室工作台。在DE中，用户可以共享数据集和工具，以与他们想要的人或多或少的人分析数据。IFactory员工开发或其他人开发的用于分析数据的工具可以与更广泛的社区共享，就像智能手机上的应用程序一样。IPLANT Collaborative目前分布在美国的三个地点；我们建议通过在基因组分析中心(TGAC)建立一个英国iPLANT节点，将这一合作扩展到国际合作。TGAC提供国家计算基础设施能力，因此非常适合为iFactory UK节点提供基础。英国的iPLANT节点将提供独立版本的iPLANT数据存储和DE，但也将链接到美国节点，以共享资源和专业知识。对于一个成功的基础设施来说，仅有物理资源是不够的：还需要随着需求的增加而使用、维护和扩展。为了展示iPLANT UK的多功能性、功能和价值，华威大学、利物浦大学和诺丁汉大学的一个专门的程序员团队将对已生成的用于单个项目的工具进行调整，以供更广泛的社区采用。三套有益于英国植物科学关键领域的工具--测序、系统生物学和图像分析--将通过iPLANT DE向全球植物研究界提供。在不到10年的时间里，iPLANT已经建立了超过18,500名用户的全球用户基础。随着这一领域的不断扩大，必须考虑iPlant未来的可持续性。英国的iFactory节点将有助于确保iFactory未来的存在和可靠性，在英国和美国之间传播专业知识和最佳实践，使英国能够为这一宝贵资源的未来方向提供投入，并为其他希望建立未来国际iFactory节点的人提供一个示范项目。通过建立iPlant UK并促进对允许用户方便地存储和分析他们的数据的资源的访问，该项目将帮助支持广泛的研究，包括利用作物自然变异的全基因组关联项目、预测生物网络和途径，以及高通量成像和图像分析服务，使研究人员更接近于弥合基因与表型的差距。

Biology is increasingly a 'big data' science as new high-throughput technologies support faster, cheaper generation of sequencing, metabolite and image data. This enables potentially exciting breakthroughs as researchers spot undiscovered patterns and make new discoveries of biological importance. However, many individual biologists, and in some areas the community as a whole, struggle to take full advantage of the data generated because of a lack of computing resource, appropriate support and technical skill. It is not only the output of data analyses, such as a models, curated datasets, or raw data, that have value to the wider community, but also the tools generated during research projects that are used to support researchers to test and validate their hypotheses. Currently these tools often remain in prototype form, for use only within the group or laboratory that generated them, because there is comparatively little standardisation and no easy means of sharing an accessible, user-friendly version of the tool. To undertake world-class bioscience, researchers therefore need to be able to store and access datasets, models and analysis tools, ideally from different locations across the globe due to the need for international collaboration. The iPlant Collaborative was funded by US agency the National Science Foundation (NSF) in 2008 to help solve these issues. The iPlant Data Store is a cloud-based storage space, accessed via iPlant's Discovery Environment (DE), a virtual work/lab bench. In the DE, users can share datasets and tools to analyse data with as many or as few people as they wish. Tools to analyse data developed by iPlant staff or built by others can be shared with the wider community, in a similar manner to 'apps' on smartphones. The iPlant Collaborative is currently distributed across three US locations; we propose to extend this into an international collaboration by building a UK iPlant node at The Genome Analysis Centre (TGAC). TGAC provides the National Capability of computational infrastructure and as such is perfectly situated to provide the foundations for the iPlant UK node. The UK iPlant node would provide independent versions of the iPlant Data Store and DE but would also be linked to the US nodes to share resources and expertise. Physical resource alone is not sufficient for a successful infrastructure: it also needs to be used, maintained and expanded as demand increases. To demonstrate the versatility, power and value of iPlant UK, a dedicated team of programmers based at the Universities of Warwick, Liverpool and Nottingham will adapt tools that have been generated for use in a single project for wider community adoption. Three suites of tools to benefit key areas of UK plant science - sequencing, systems biology and image analysis - will be made available to the global plant research community via the iPlant DE.In less than 10 years, iPlant has built a global user base of over 18,500 users. As this continues to expand, iPlant's future sustainability must be considered. A UK iPlant node will help ensure the future existence and reliability of iPlant, spread expertise and best practice between the UK and US, allow the UK to input to the future direction of this valuable resource and provide an exemplar project to others wishing to establish future international iPlant nodes. By establishing iPlant UK and promoting access to a resource that allows users to readily store and analyse their data, this project will help support a wide range of research including genome-wide association projects exploiting natural variation in crops, predicting biological networks and pathways, and the high-throughput imaging and image analysis services that take researchers one step closer to bridging the genotype to phenotype gap.