The MRC Consortium for Medical Microbial Bioinformatics

沃里克大学和斯旺西大学与伯明翰大学和卡迪夫大学合作，提出了一项资本支出，招聘和培训计划，以创建MRC医学微生物生物信息学联盟，这是一个最先进的跨学科设施，由Mark Pallen教授领导（沃里克的医学博士）和斯旺西的萨姆·谢泼德博士，供学术界使用，工业界和医疗保健界，将提高区域和国家在微生物生物信息学方面的能力和基础设施，了解具有医学重要性的细菌。依据：微生物病原体仍然是人类的主要威胁。此外，人体微生物组-宿主相关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学状况（例如肥胖症）中也是如此。因此，利用医学生物信息学研究微生物基因、基因组和宏基因组是一个独特的挑战，也是响应MRC号召的一个独特焦点。我们并没有瞄准人类基因组这个固定的、相对容易处理的目标，而是专注于来自数百种细菌病原体和数千种常见物种的基因组信息：这是一个由数百万个基因组成的分布式动态系统，至少比人类基因组大两个数量级。我们的四个研究活跃的大学位于英国的邻近地区，从而提供了一个初始的地理凝聚力，以促进社区建设和思想交流的联盟，并巩固治理的手续。在成立之初，该联盟将通过密集的合作网络，合议制以及新合作伙伴的申请流程，从全球范围内受益，并将很快以可扩展的方式发展，以拥抱国家职权范围。该联盟将建立在个人研究卓越的跟踪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了独特的贡献。通过这一举措，我们将招募三名来自学科或国家以外职业的高素质人才进入微生物生物信息学研究金。我们已经从主办机构的杠杆支持，把这些研究员在任期轨道。所有三名研究员将通过研究、培训和管理作用以及推进自己的尖端研究方案，为联合会的目标作出贡献。基于对并行化和云计算的兴趣，我们将在威尔士和西米德兰兹郡开发一个可扩展的基础设施，为英国微生物学研究社区提供一个敏捷，可扩展的系统。我们将开发一个雄心勃勃的和令人兴奋的培训计划，包括训练营，黑客马拉松，研讨会，模块和课程，适合从专业生物信息学家到大学生的广泛用户。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，鼓励知识转让和传播最佳做法。每月、每季度和每年将举行不同种类和规模的会议。年会，与学术和管理的组成部分，将受益于我们的外部指导小组的参与。我们将利用政府注资和外部资助的研究活动，以“加强我们的系统”，确认我们所建立的设施按计划运作和/或启动对我们的基础设施的迭代优化。我们相信，该联盟将通过机构承诺和筹集额外的研究资金来实现自我维持。

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.