COMMUNITY CYBERINFRASTRUCT FOR ADV MAR MICRO ECOL RES & ANALY

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 加州电信和信息技术研究所(Calit2)[1]和J·克雷格·文特尔研究所(JCVI)[2]联合提议，利用最先进的计算数据网格、光学网络和计算技术，开发一个最先进的基因组数据、分析和合成中心，致力于研究生物在自然生态系统中发挥作用的复杂性的科学家的需求。迫切需要这样一个中心，以实现从有机基因组学向环境元基因组学的过渡。正如分子生物学和最近的计算生物学从众多研究微生物学现象的学科的相互作用中出现一样，海洋微生物生态学正在成为这种创造性、跨学科能量的焦点，正在成为基因组学和信息技术交界处创新的前沿。 随着鸟枪测序应用于整个微生物群落，基因组学在生物发现方面的发展速度和力量正在迅速增加[3]。摩尔基金会[4]、美国能源部(DOE)和国家科学基金会(NSF)正在资助一些关于自然生态系统的初步元基因组研究。 其中规模最大的是文特尔研究所的魔法师二号考察队[5]，他们每隔200英里对全球海洋微生物群落进行采样。虽然从探险队第一站的序列数据中添加到GenBank[6]的碱基数量只占目前总数的几个百分点，但预测的蛋白质数量将翻一番。此外，在GenBank目前发现的约4000个基因家族的基础上，还将增加约6000个新基因家族。 从培养物中测序的基因组数量也在迅速增加。例如，在摩尔基金会的资助下，文特尔研究所仅在今年就将对超过75种海洋微生物的基因组进行测序[7]。能源部的联合基因组研究所(JGI)[8]每年测序超过50个。 这些新的序列、基因和基因家族，以及相关的环境数据，为更好地了解自然生态系统的功能提供了巨大的潜力。环境元基因组学研究了可能存在于空间和时间点上的数千个物种之间的相互作用。每个单独的序列不再仅仅是基因组的一部分。它是整个生物群落的一部分。现在可以从生态科学的世界观来考虑每个单独的序列：群落其余部分的组成，发现它的环境条件，以及它与在其他时间和地点发现的其他物种的关系。更重要的是，它提供了一幅更完整的图景，提供了许多来自实验室培养中不可持续的物种的基因组，而这些物种只存在于其本土环境中。 这些信息丰富的元基因组样本的爆炸性增长需要一个创新的体系结构，它在数据存储、访问、分析和合成中使用新兴的数字基础设施概念，而这些概念在当前的基因序列资源中是不可用的。该项目的总体目标是创建一个社区资源和环境基因组学中心，以促进和创造我们对海洋和其他自然环境中的微生物生态以及进化生物学知识的革命性进步。为此，拟建的中心将汇聚高通量DNA测序和元基因组分析工具等新技术的领导者，以及光耦合计算、新兴网格中间件和用户工作空间方面的网络基础设施创新。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The California Institute for Telecommunications and Information Technology (Calit2) [1] and the J. Craig Venter Institute (JCVI) [2] jointly propose to develop a state-of-the-art genomics data, analysis, and synthesis center, using the most advanced computational data grid, optical networking, and computing technologies, devoted to the needs of scientists studying the complexity of organisms as they function in natural ecosystems. Such a center is needed urgently to enable the transition from organismal genomics to environmental metagenomics. Just as molecular biology, and more recently computational biology, emerged from the interplay of numerous disciplines looking at microbiological phenomena, marine microbial ecology is becoming a focus of such creative, interdisciplinary energy, a frontier for innovation at the interface of genomics and information technology. The pace of development and the power of genomics for biological discovery are increasing rapidly with the application of shotgun sequencing to entire microbial communities [3]. The Moore Foundation [4], the U.S. Department of Energy (DOE), and the National Science Foundation (NSF) are funding some initial metagenomic studies of natural ecosystems. The largest of these is the Venter Institute's Sorcerer II Expedition [5], sampling marine microbial communities every 200 miles around the globe. Though the number of bases that will be added to GenBank [6] from the sequence data from the first leg of the expedition is but a few percent of the current total, the number of predicted proteins will double. Moreover, about 6,000 new gene families will be added to the approximately 4,000 found in GenBank today. The number of genomes sequenced from culture is also increasing rapidly. For example, the Venter Institute, with Moore Foundation funding, will sequence the genomes of more than 75 marine microbes this year alone [7]. DOE's Joint Genome Institute (JGI) [8] sequences more than 50 per year. These new sequences, genes, and gene families, together with associated environmental data, offer tremendous potential to understand better the functioning of natural ecosystems. Environmental metagenomics examines the interplay of perhaps thousands of species present at a point in space and time. Each individual sequence is no longer just a piece of a genome. It is a piece of an entire biological community. Each individual sequence can now be considered from the worldview of the ecological sciences: the composition of the rest of the community, the environmental conditions in which it is found, and its relationships with other species with which it is found at other times and places. More importantly, it provides a more complete picture by providing many genomes from species not sustainable in laboratory cultures but only present in their native environments. The explosion of these information-rich metagenomic samples requires an innovative architecture that uses emerging Cyberinfrastructure concepts in data storage, access, analysis, and synthesis that are simply not available in the current gene sequence resources. The overarching goal of this project is to create a community resource and center for environmental genomics that will facilitate and create revolutionary advances in our knowledge of microbial ecology in marine and other natural environments, and of evolutionary biology. To this end, the proposed Center will bring together leaders in the new technologies of high-throughput DNA sequencing, and metagenomic analysis tools on the one hand, and Cyberinfrastructure innovations in optically coupled computing, emerging Grid middleware, and user workspaces on the other.