COMMUNITY CYBERINFRASTRUCT FOR ADV MAR MICRO ECOL RES & ANALY

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 研究中心，而研究中心不一定是研究者所在的机构。 加州电信和信息技术研究所（Calit 2）[1]和J.克雷格文特尔研究所（JCVI）[2]联合提议开发一个最先进的基因组学数据、分析和合成中心，使用最先进的计算数据网格、光学网络和计算技术，致力于满足科学家研究生物体在自然生态系统中的复杂性的需求。 迫切需要这样一个中心，以实现从生物基因组学到环境宏基因组学的过渡。正如分子生物学和最近的计算生物学是从研究微生物现象的众多学科的相互作用中产生的一样，海洋微生物生态学正在成为这种创造性的跨学科能量的焦点，成为基因组学和信息技术界面上的创新前沿。 随着鸟枪测序技术在整个微生物群落中的应用，基因组学在生物发现中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）正在资助一些自然生态系统的初步宏基因组研究。 其中规模最大的是文特尔研究所的巫师二号考察队[5]，在地球仪周围每隔200英里对海洋微生物群落进行采样。 虽然从第一段考察的序列数据中添加到GenBank中的碱基数量只占当前总数的百分之几，但预测的蛋白质数量将增加一倍。 此外，大约6,000个新的基因家族将被添加到今天在基因库中发现的大约4,000个基因家族中。 从培养物中测序的基因组数量也在迅速增加。例如，文特尔研究所在摩尔基金会的资助下，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]。 美国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。环境宏基因组学研究可能存在于空间和时间上的数千个物种的相互作用。 每个单独的序列不再只是基因组的一部分。 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一个单独的序列：群落其余部分的组成，它被发现的环境条件，以及它与其他物种的关系，这些物种在其他时间和地点被发现。更重要的是，它提供了一个更完整的图片，提供了许多基因组物种不可持续的实验室培养，但只存在于其原生环境。 这些信息丰富的宏基因组样本的爆炸需要一个创新的架构，该架构在数据存储，访问，分析和合成中使用新兴的网络基础设施概念，这些概念在当前的基因序列资源中根本不可用。 该项目的总体目标是创建一个环境基因组学的社区资源和中心，这将促进和创造我们在海洋和其他自然环境中的微生物生态学知识的革命性进步，以及进化生物学。为此，拟议中的中心将汇集高通量DNA测序和宏基因组分析工具的新技术的领导者，以及光耦合计算，新兴网格中间件和用户界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.