COMMUNITY CYBERINFRASTRUCT FOR ADV MAR MICRO ECOL RES & ANALY

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。加州电信和信息技术研究所（Calit2）[1]和J. Craig Venter研究所（JCVI）[1]联合提议开发一个最先进的基因组数据、分析和合成中心，使用最先进的计算数据网格、光网络和计算技术，致力于满足科学家研究生物在自然生态系统中功能复杂性的需求。为了实现从生物基因组学到环境宏基因组学的过渡，迫切需要这样一个中心。正如分子生物学，以及最近的计算生物学，从众多研究微生物现象的学科的相互作用中涌现出来一样，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，是基因组学和信息技术界面创新的前沿。随着霰弹枪测序在整个微生物群落中的应用，基因组学的发展速度和生物学发现的力量正在迅速增加。摩尔基金会（Moore Foundation）、美国能源部（DOE）和美国国家科学基金会（NSF）正在资助一些初步的自然生态系统宏基因组研究。其中最大的是文特尔研究所的魔法师二号探险b[5]，在全球每200英里采样一次海洋微生物群落。虽然从探险第一站的序列数据中添加到GenBank[6]的碱基数量只是目前总数的几个百分点，但预测的蛋白质数量将增加一倍。此外，在基因库现有的约4000个基因家族基础上，还将增加约6000个新的基因家族。从培养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，仅今年一年就将对超过75种海洋微生物的基因组进行测序。美国能源部联合基因组研究所（JGI）每年进行50多次测序。这些新的序列、基因和基因家族，连同相关的环境数据，为更好地理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的是在某个时空点上可能存在的数千种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，每个单独的序列都可以从生态科学的世界观来考虑：群落其余部分的组成，发现它的环境条件，以及它与其他时间和地点发现的其他物种的关系。更重要的是，它提供了许多物种的基因组，这些物种在实验室培养中不可持续，但只存在于它们的原生环境中，从而提供了一个更完整的图景。这些信息丰富的宏基因组样本的爆炸式增长需要一种创新的架构，该架构在数据存储、访问、分析和合成方面使用新兴的网络基础设施概念，而这些概念在当前的基因序列资源中根本无法获得。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，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以及进化生物学方面的知识的革命性进步。为此，该中心一方面将汇集高通量DNA测序和宏基因组分析工具等新技术的领导者，另一方面将汇集光耦合计算、新兴网格中间件和用户工作区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.