The MRC Consortium for Medical Microbial Bioinformatics

华威大学和斯旺西大学与伯明翰大学和加的夫大学合作，提出了一项资本支出、招聘和培训计划，以创建医学微生物生物信息学MRC联盟，这是一个最先进的跨学科设施，由马克·帕伦教授(华威大学的医学博士)和萨姆·谢泼德博士在斯旺西领导，供学术、工业和医疗保健社区使用，将加强地区和国家在微生物生物信息学方面的能力和基础设施，并提高我们对细菌医学重要性的理解。基本原理：微生物病原体仍然是人类生存的主要威胁。此外，人类微生物群--与宿主相关的微生物及其基因的丰富和动态群落--现在已知在健康和疾病之间的平衡中发挥决定性作用，即使在通常不被认为是微生物起源的医疗条件下(例如肥胖)。因此，利用医学生物信息学来研究微生物基因、基因组和亚基因组是一个独特的、尚未满足的挑战，也是对这一MRC呼吁的响应中的一个独特的焦点。我们没有瞄准固定的、相对容易处理的人类基因组目标，而是专注于来自数百种细菌病原体和数千种共生物种的基因组信息：一个由数百万个基因组成的分布式动态系统，至少比人类基因集大两个数量级。我们的四所研究活跃的大学位于英国的邻近地区，因此为联盟提供了初步的地理凝聚力，这将促进社区建设和思想交流，并为治理的正式程序奠定基础。在成立之初，该联盟将通过密集的合作网络和联合领导，受益于全国和全球的影响，并将通过申请新合作伙伴的程序，很快以可扩展的方式发展，以接受国家的职责。该联盟将建立在个人研究的卓越记录和令人印象深刻的医疗微生物学和生物信息学机构投资的基础上，所有合作伙伴都做出独特的贡献。通过这一计划，我们将招募三名才华横溢的人加入微生物生物信息学奖学金，这些人来自学科或国家以外的职业。我们利用主办组织的支持，将这些研究员安排在终身教职的轨道上。所有三名研究员都将通过研究、培训和管理角色，以及推动他们自己的尖端研究计划，为联盟的目标做出贡献。基于对并行和云计算的兴趣，我们将在威尔士和西米德兰兹郡开发一个分布式计算基础设施，为英国微生物学研究界提供一个灵活、可扩展的系统。我们将制定一个雄心勃勃和令人兴奋的培训计划，包括训练营、黑客松、工作坊、模块和课程，适合从专业生物信息学家到本科生的广泛用户。我们将通过社区建设活动加强区域、国家和国际微生物生物信息学研究，鼓励知识转移和传播最佳实践。不同种类和规模的会议将按月、按季和按年举行。年会包括学术和管理部分，将受益于我们外部指导小组的参与。我们将利用注资资金和外部资助的研究活动来“强调我们的系统”，确认我们创建的设施按计划工作，和/或启动对我们基础设施的迭代改进。我们相信，该财团将通过机构承诺和招募更多研究资金，实现自给自足。

The UNIVERSITY OF WARWICK and SWANSEA UNIVERSITY, in partnership with the UNIVERSITY OF BIRMINGHAM and CARDIFF UNIVERSITY, propose a programme of capital expenditure, recruitment and training to create the MRC CONSORTIUM FOR MEDICAL MICROBIAL BIOINFORMATICS, a state-of-the-art interdisciplinary facility, led by Professor Mark Pallen (an MD PhD at Warwick) and Dr Sam Sheppard in Swansea, for use by the academic, industrial and healthcare communities that will enhance regional and national capability and infrastructure in microbial bioinformatics and improve our understanding of bacteria of medical importance. RATIONALE: Microbial pathogens still present a MAJOR EXISTENTIAL THREAT to humanity. In addition, the HUMAN MICROBIOME - the rich and dynamic community of host-associated microorganisms and their genes - is now known to play a decisive role in the balance between health and disease, even in medical conditions not usually considered as microbial in origin (e.g. obesity). Harnessing medical bioinformatics to the study of microbial genes, genomes and metagenomes thus represents a DISTINCTIVE UNMET CHALLENGE and a UNIQUE FOCUS AMONG RESPONSES TO THIS MRC CALL. Rather than taking aim at the fixed, relatively tractable target of the human genome, we focus instead on genomic information derived from HUNDREDS OF BACTERIAL PATHOGENS and THOUSANDS OF COMMENSAL SPECIES: a distributed and dynamic system of MANY MILLIONS OF GENES, at least two orders of magnitude larger than the human gene set. Our four research-active universities are located in neighbouring regions of the UK, thus providing an initial GEOGRAPHICAL COHESION to the Consortium that will facilitate community building and the exchange of ideas, and underpin the formalities of governance. At its inception, the Consortium will benefit from a NATIONAL AND GLOBAL REACH through a dense network of collaborations, collegiality and, through an application process for new partners, will soon grow in a scalable fashion to embrace a national remit. The Consortium will build on TRACK RECORDS OF INDIVIDUAL RESEARCH EXCELLENCE and impressive INSTITUTIONAL INVESTMENT in medical microbiology and bioinformatics with all partners making a distinctive contribution. Through this initiative we will recruit THREE HIGHLY TALENTED INDIVIDUALS into microbial bioinformatics fellowships from careers outside the discipline or the country. We have LEVERAGED SUPPORT from the host organisations to place these research fellows on a TENURE TRACK. All three fellows will contribute to the goals of the Consortium through research, training and management roles as well as pushing forward their own cutting-edge research programmes. Building on interests in parallelisation and cloud computing, we will develop a DISTRIBUTED COMPUTING INFRASTRUCTURE in Wales and the West Midlands that will provide an agile, scalable system for the UK microbiology research community.We will develop an ambitious and exciting TRAINING PROGRAMME that will include bootcamps, hackathons, workshops, modules and courses, suitable for a wide range of users from professional bioinformaticians to undergraduate students.We will strengthen regional, national and international microbial bioinformatics research through COMMUNITY-BUILDING ACTIVITIES, encouraging knowledge transfer and dissemination of best practice. Meetings of different sorts and scale will be held monthly and quarterly and annually. The Annual Meeting, with an academic and management component, will benefit from participation by our external Steering Group. We will exploit pump-priming funds together with externally funded research activities to "stress our systems", confirming that the facilities that we have created work as planned and/or priming iterative refinements to our infra-structure. We are confident that the consortium will become self-sustaining through institutional commitments and the recruitment of additional research funding.