INBRE BIOINFORMATICS CORE

INBRE 生物信息学核心

• 批准号: 7960163
• 负责人: KARL V. STEINER
• 金额: $ 85.76万
• 依托单位: UNIVERSITY OF DELAWARE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-01 至 2010-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7960163
• 关键词: Administrative Supplement; Architecture; Area; Award; Baltimore; Bioinformatics; Biological Sciences; Biomedical Research; Biometry; Biotechnology; Bite; Canada; Caring; Code; Collaborations; Communication; Communities; Complex; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Computer Systems; Computer software; Computers; Core Facility; Data; Data Set; Databases; Delaware; Development; Disasters; Educational workshop; Electron Microscope; Electronic Mail; Engineering; Faculty; Foundations; Funding; Genomics; Goals; Grant; Graph; Housing; Human Resources; Image; Imagery; Individual; Institutes; Institution; Internet; Joints; Lead; Learning; Life; Linux; Location; Maine; Mass Spectrum Analysis; Medical; Memory; Metric; Microscope; New England; New Hampshire; Nucleotides; Online Systems; Outcome; Performance; Persons; Philadelphia; Population; Positioning Attribute; Production; Progress Reports; Protocols documentation; Publishing; Quartz; Reading; Recovery; Research; Research Infrastructure; Research Personnel; Research Project Grants; Resources; Rhode Island; Running; Scanning; Scientist; Secure; Services; Site; Solutions; Source; Stream; Students; Surveys; Sustainable Development; System; Systems Biology; Techniques; Technology; Time; United States National Institutes of Health; Universities; Update; Vermont; Vertebral column; Videoconferences; Videoconferencing; Work; Writing; base; bioimaging; cluster computing; collaboratory; college; computing resources; cyber infrastructure; experience; falls; image visualization; improved; instrument; instrumentation; interest; meetings; member; multi-photon; next generation; open source; parallel computing; posters; programs; science and society; symposium; tool; web interface

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. Delaware INBRE Annual Progress Report (APR) 2008 Grant No. 5P20RR016472-07 Bioinformatics Core The goal of the Delaware INBRE Bioinformatics Core is to position Delaware to provide resources and expertise in the areas of bioinformatics, computational and systems biology to enable Delaware's faculty to become nationally competitive in biomedical research. To meet that goal bioinformatics labs have been implemented at all of the academic partner institutions, i.e. the Delaware Biotechnology Institute at the University of Delaware (DBI), Delaware State University (DSU), Wesley College and Delaware Technical & Community College (DTCC). In addition, a unique network of biomedical visualization centers has been installed at Christiana Care, DBI, DSU and DTCC. The Bioinformatics (BioIT) Center at DBI serves as the hub for many of the activities in the bioinformatics core. It is managed by Dr. Douglas O'Neal and provides professionally expertise in high-performance computation, database analysis and image visualization. The BioIT Center has integrated significant hardware and software resources into a reliable and unified system. Within this system, compute, database and visualization servers are transparently working with each other to provide secure access to researchers across the INBRE Network. The BioIT Center continues to provide resources for computing and database needs of INBRE researchers, with about ten research groups running code on the compute cluster, four groups using the database cluster, four groups hosting their servers in the Core's computer room, three groups utilizing the Visualization studio and the Core's email and web servers servicing a broad range of users. Accomplishments of the Bioinformatics Core in Year 7 include: Development of a Statewide Cyberinfrastructure Plan + Delaware research institutions have developed a plan to improve the State's cyber-infrastructure to better meet the needs of the INBRE community. This plan is focused on five main objectives: (1) Strengthen capacity and capability of cyber-knowledgeable faculty and staff; (2) Provide a strong computational capability that is easily accessible to all members in the Network; (3) Develop regional collaborations to take advantage of expertise and capabilities in partner states; (4) Develop a high-throughput genomics research capability; and (5) Provide collaborative research capabilities at the desktop level. + Due to its central location on the Mid-Atlantic Coast and close proximity to major population centers such as Philadelphia, PA and Baltimore, MD, Delaware's cyberinfrastructure is well positioned. The graph provided above shows an overview of the status of Delaware's network connectivity. With support by the NIHINBRE and the NSFEPSCoR RII program, all of the partner institutions have put in place dedicated centers or classrooms to support bioinformatics research and learning activities. In comparison to many other IDeA states, Delaware's connectivity to the Nation's broadband networks (Abilene and National LambdaRail) is in good condition. There is, however, a continuing need to further improve desktop access for researchers at many of Delaware's INBRE partner institutions. The most pressing need is for more cyberinfrastructure personnel that can provide faculty and students with the necessary expertise to utilize many of the tools already available to Delaware researchers, including complex data visualization and access to parallel computing and database resources both in-state and through the grid. Listed below are updates to each of the strategic objectives outlined above: (1) Strengthening Bioinformatics Faculty at Delaware Institutions + The University of Delaware is currently searching for the Edward G. Jefferson Endowed Chair in Bioinformatics and Computational Biology, who will have the responsibility to build a coherent bioinformatics network across UD and across the State and lead the search for three additional junior faculty members. This initiative will provide much needed expertise for the growing INBRE Network. These new faculty members will be augmented by an experienced group of staff scientists and engineers at the DBI Bioinformatics (BioIT) Center. + Delaware State University is finalizing plans to hire two new faculty members with expertise in bioinformatics and biostatistics. These two faculty members will collaborate with each other and with research teams across institutions. The biostatistics faculty fills a much-needed gap in faculty expertise at DSU. The bioinformaticist will facilitate DSU goals by implementing technologies, integrating into existing networks, and collaborating with DSU experimentalists to incorporate bioinformatics techniques and resources into their research. These searches will be launched within the next two years. (2) Bioinformatics Infrastructure and Management Upgrade + Database services have been migrated to a cluster of six servers allowing for higher performance and reliability. Performance gains on single-server applications have been seen but major speedups are possible with the parallelization of database queries across multiple servers. In one production application, query times have been reduced by two orders of magnitude by re-writing the application to use multiple servers in parallel. + A database system has been installed for use by the Bioimaging Core, where data from various microscopes can be uploaded, annotated, and shared though a web interface. Approximately .5 TB of image data is currently being shared though this system. + As described above, the Linux compute cluster has seen incremental upgrades. Seven of the original dual-core/2GB ram 32-bit servers have been replaced with quad-core/8GB ram 64-bit systems. Four more of the original servers were later replaced with one 16-core/64GB ram 64-bit server and one 16-core/128GB ram 64-bit server. The original file server for the cluster has been replaced with a newer server with higher hardware redundancy. Use of the 64-bit servers has allowed calculations on problems that were not possible with the architecture restrictions imposed by 32-bit hardware. + Backup services to on-line storage have been extended to all data within the Core. An off-site copy of the backup data is created in real-time to allow for disaster recovery. + The Bioinformatics Core participated in the Core Center Open House that was held at DBI on October 5, 2007. The Open House even included presentations by all Core Center directors and was followed by tours and demonstrations in the centers. The Open House presentations were video-streamed live for viewing by interested researchers who were not able to attend. + Core personnel implemented several programs to aid in evaluating grant metrics, creating tools to create, publish, and evaluate data from web-based surveys and on-line databases of information on persons associated with DBI grants. + A web-based system for accepting student resumes and matching them to open research positions was brought online in the past year. Research Accomplishments and Ongoing Projects: + The BioIT Center's Manager, Dr. Douglas O'Neal, was invited to participate on the Bioinformatics Panel at the Northeast Regional Life Sciences Core Directors Meeting held November 7-9, 2007 at Cornell University. This meeting brought together Core Directors from the Northeast Region as well as several other states and Canada. + The BioIT Center's Database Programmer, Dr. Mihailo Kaplarevic, attended the Life Sciences Society Computational Systems Bioinformatics Conference held at San Diego August 13-17, 2007, presenting a poster titled "Advanced Framework for Environmental Metagenome Analysis." (3) NENI  A Regional Cyberinfrastructure Collaboration among IDeA States + The Delaware INBRE is leading a regional effort called Northeast Network Initiative (NENI) to systemically improve inter-institutional collaborations among academic and biomedical institutions in New Hampshire, Maine, Rhode Island, Vermont and Delaware. The NENI initiative will lead to the development of sustainable biomedical research capabilities by significantly enhancing connectivity for academic and medical institutions in the New England States and Delaware  the members of the Northeastern IDeA Network. This fundamental infrastructure enhancement is required to provide a critical backbone for new collaborative research projects and provide remote access to core facilities in such areas as bioinformatics, bioimaging, sequencing or mass spectroscopy; facilitate remote videoconferencing and on-line streaming of workshops and seminars; and the development of joint research projects with faculty and students at institutions across the Northeastern States in the IDeA Network and across the nationwide IDeA community. + The first regional NENI Workshop was held during the 2nd Northeast Regional IDeA meeting in Burlington, VT on August 17, 2007. During this meeting the members of the NENI Executive Council presented an overview of the Initiative and then individual updates on the needs, status and activities within each NENI state. + As a direct outcome of the workshop and the NENI initiative, the NENI states competed for an INBRE Administrative Supplement in fall 2007 and secured about $550k from NIH-NCRR to launch the initiative. Delaware received $160,000 to upgrade network infrastructure at Delaware State University and to install a high-memory compute server in the BioIT center at DBI. The remainder of the funds has been awarded to Maine. (4) High-throughput Genomics Research Capability + A high-throughput genomics research capability is being installed at DBI to significantly upgrade the capabilities of the Network. To meet this objective, a Sequence-by-Synthesis (SBS) instrument based on Solexa's Massively Parallel Signature Sequencing (MPSS") technology has been ordered with funding provided by the NSF-EPSCoR program and a grant from the Unidel Foundation. This "next-generation" instrument will generate large amounts of short reads (35 to 50 nucleotides) and thus creates significant amounts of data per instrument run. This makes the technology ideal for rapidly and economically developing datasets that can be compared against an existing genomic database or where the potential for chimeric sequence assembly is low. To accommodate this data-influx, a very-high-memory database server, funded through the INBRE Administrative Supplement described above, has been installed in the BioIT Center to provide the bioinformatics pipeline required for data handling and analysis. (5) Collaborative Research Capabilities at the Desktop Level + Despite its small size, there is a growing need in Delaware for improving cyber-based communications among researchers and educators. Polycom-based videoconferencing systems that utilize the H.323 protocol and facilitate classroom-based or group discussions are in place at most of the participating institutions due to an NIHINBRE Supplement awarded in 2005. We plan to build on this base by providing desktop videoconferencing access to individual researchers through H.323-compatible systems such as Ekiga or NetMeeting for PCs, or XMeeting for Mac OSX. Many of these solutions are open-source and require only a camera and microphone at the user level and sufficient bandwidth on the institutional level. In addition, we plan to expand the use of collaboratories that allow researchers to access high-end instrumentation located at core instrumentation centers. The DBI Bioimaging Center already uses Quartz PCI collaborative software on its multi-photon and field emission scanning electron microscopes to provide remote access to these unique and complex instruments for researchers across the State.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 特拉华州 INBRE 年度进展报告 (APR) 2008 授权号 5P20RR016472-07 生物信息学核心 特拉华州 INBRE 生物信息学核心的目标是让特拉华州在生物信息学、计算和系统生物学领域提供资源和专业知识，使特拉华州的教师在生物医学研究方面具有全国竞争力。 为了实现这一目标，所有学术合作机构都建立了生物信息学实验室，即特拉华大学特拉华生物技术研究所 (DBI)、特拉华州立大学 (DSU)、韦斯利学院和特拉华技术与社区学院 (DTCC)。 此外，Christiana Care、DBI、DSU 和 DTCC 还安装了独特的生物医学可视化中心网络。 DBI 的生物信息学 (BioIT) 中心是生物信息学核心许多活动的中心。 它由 Douglas O'Neal 博士管理，提供高性能计算、数据库分析和图像可视化方面的专业知识。 BioIT中心将重要的硬件和软件资源集成到一个可靠且统一的系统中。在该系统中，计算、数据库和可视化服务器透明地相互协作，为研究人员提供跨 INBRE 网络的安全访问。 BioIT 中心继续为 INBRE 研究人员的计算和数据库需求提供资源，大约有十个研究小组在计算集群上运行代码，四个小组使用数据库集群，四个小组在核心机房托管服务器，三个小组利用可视化工作室以及核心的电子邮件和网络服务器为广泛的用户提供服务。 第七年生物信息学核心的成就包括： 制定全州网络基础设施计划 + 特拉华州研究机构制定了一项改善该州网络基础设施的计划，以更好地满足 INBRE 社区的需求。 该计划重点关注五个主要目标：（1）加强具有网络知识的教职员工的能力和能力； (2) 提供强大的计算能力，让网络中的所有成员都能轻松访问； (3) 发展区域合作，利用伙伴国的专业知识和能力； （4）培养高通量基因组学研究能力； (5) 提供桌面层面的协作研究能力。 + 由于特拉华州位于大西洋中部海岸的中心位置，并且靠近宾夕法尼亚州费城和马里兰州巴尔的摩等主要人口中心，因此特拉华州的网络基础设施地理位置优越。上面提供的图表显示了特拉华州网络连接状态的概述。 在 NIH INBRE 和 NSF EPSCoR RII 项目的支持下，所有合作机构都设立了专门的中心或教室来支持生物信息学研究和学习活动。 与许多其他 IDeA 州相比，特拉华州与国家宽带网络（阿比林和 National LambdaRail）的连接状况良好。然而，仍然需要进一步改善特拉华州许多 INBRE 合作机构的研究人员的桌面访问。最迫切的需求是需要更多的网络基础设施人员，为教师和学生提供必要的专业知识，以利用特拉华州研究人员现有的许多工具，包括复杂的数据可视化以及对州内和通过特拉华州的并行计算和数据库资源的访问。网格。 下面列出了上述每项战略目标的更新： (1) 加强特拉华州机构的生物信息学师资力量 + 特拉华大学目前正在寻找爱德华·G·杰斐逊生物信息学和计算生物学讲座教授，他将负责在特拉华大学和全州建立一个连贯的生物信息学网络，并领导寻找另外三名初级教员。这一举措将为不断发展的 INBRE 网络提供急需的专业知识。 DBI 生物信息学 (BioIT) 中心经验丰富的科学家和工程师团队将补充这些新的教职人员。 + 特拉华州立大学正在敲定聘用两名具有生物信息学和生物统计学专业知识的新教员的计划。这两名教师将相互合作，并与跨机构的研究团队合作。 生物统计学教师填补了 DSU 教师专业知识急需的空白。生物信息学家将通过实施技术、融入现有网络以及与 DSU 实验人员合作将生物信息学技术和资源纳入他们的研究来促进 DSU 的目标。 这些搜索将在未来两年内启动。 (2)生物信息基础设施和管理升级 + 数据库服务已迁移到由六台服务器组成的集群，从而实现更高的性能和可靠性。 单服务器应用程序的性能提升已经可见，但通过跨多个服务器的数据库查询并行化，可以实现大幅加速。 在一个生产应用程序中，通过重写应用程序以并行使用多个服务器，查询时间已减少了两个数量级。 + 已安装数据库系统供生物成像核心使用，可以通过网络界面上传、注释和共享来自各种显微镜的数据。 目前通过该系统共享大约 0.5 TB 的图像数据。 + 如上所述，Linux 计算集群已经进行了增量升级。 七台原来的双核/2GB 内存 32 位服务器已替换为四核/8GB 内存 64 位系统。 另外四台原始服务器后来被替换为一台 16 核/64GB 内存 64 位服务器和一台 16 核/128GB 内存 64 位服务器。 集群的原始文件服务器已替换为具有更高硬件冗余的较新服务器。 使用 64 位服务器可以解决因 32 位硬件的架构限制而无法解决的问题。 + 在线存储的备份服务已扩展到核心内的所有数据。 实时创建备份数据的异地副本以实现灾难恢复。 + 生物信息学核心参加了 2007 年 10 月 5 日在 DBI 举行的核心中心开放日。开放日甚至包括所有核心中心主任的演讲，随后是在中心的参观和演示。 开放日的演示进行了现场视频直播，供未能参加的感兴趣的研究人员观看。 + 核心人员实施了多项计划来帮助评估拨款指标，创建工具来创建、发布和评估来自与 DBI 拨款相关人员信息的网络调查和在线数据库的数据。 + 去年上线了一个基于网络的系统，用于接受学生简历并将其与空缺研究职位进行匹配。 研究成果和正在进行的项目： + BioIT 中心经理 Douglas O'Neal 博士受邀参加 2007 年 11 月 7 日至 9 日在康奈尔大学举行的东北地区生命科学核心董事会议的生物信息学小组。 这次会议汇集了来自东北地区以及其他几个州和加拿大的核心董事。 + BioIT 中心的数据库程序员 Mihailo Kaplarevic 博士出席了 2007 年 8 月 13 日至 17 日在圣地亚哥举行的生命科学学会计算系统生物信息学会议，并发表了题为“环境宏基因组分析的高级框架”的海报。 (3) NENI IDeA 成员国之间的区域网络基础设施合作 + 特拉华州 INBRE 正在领导一项名为东北网络计划 (NENI) 的区域性工作，旨在系统地改善新罕布什尔州、缅因州、罗德岛州、佛蒙特州和特拉华州的学术和生物医学机构之间的机构间合作。 NENI 倡议将通过显着增强东北 IDeA 网络成员新英格兰州和特拉华州学术和医疗机构的连通性，促进可持续生物医学研究能力的发展。 这种基础设施的增强需要为新的合作研究项目提供关键支柱，并提供对生物信息学、生物成像、测序或质谱等领域核心设施的远程访问；促进远程视频会议和讲习班和研讨会的在线直播；与东北各州机构的 IDeA 网络和全国 IDeA 社区的教师和学生开展联合研究项目。 + 第一届区域 NENI 研讨会于 2007 年 8 月 17 日在佛蒙特州伯灵顿举行的第二届东北地区 IDeA 会议期间举行。在这次会议上，NENI 执行委员会成员概述了该计划，然后介绍了需求、现状的个人最新情况以及每个 NENI 州内的活动。 + 作为研讨会和 NENI 倡议的直接成果，NENI 州于 2007 年秋季争夺 INBRE 行政补充，并从 NIH-NCRR 获得了约 55 万美元来启动该倡议。 特拉华州获得了 160,000 美元，用于升级特拉华州立大学的网络基础设施，并在 DBI 的 BioIT 中心安装高内存计算服务器。 其余资金已拨给缅因州。 (4) 高通量基因组研究能力 + DBI 正在安装高通量基因组学研究能力，以显着提升网络的能力。 为了实现这一目标，我们已在 NSF-EPSCoR 计划提供的资金和 Unidel 基金会的资助下订购了基于 Solexa 大规模并行特征测序 (MPSS") 技术的合成测序 (SBS) 仪器。 “一代”仪器将生成大量短读段（35 至 50 个核苷酸），从而在每次仪器运行时创建大量数据。这使得该技术非常适合快速、经济地开发数据集，可以与现有基因组数据库或嵌合序列组装潜力较低的情况进行比较，为了适应这种数据流入，BioIT 中安装了由上述 INBRE 管理补充资助的超高内存数据库服务器。中心提供数据处理和分析所需的生物信息学管道。 （五）桌面层面的协同研究能力 + 尽管特拉华州面积较小，但改善研究人员和教育工作者之间基于网络的通信的需求日益增长。由于 2005 年授予的 NIH INBRE 补充协议，大多数参与机构都采用了基于 Polycom 的视频会议系统，该系统利用 H.323 协议并促进课堂或小组讨论。我们计划在此基础上提供桌面通过 H.323 兼容系统（例如适用于 PC 的 Ekiga 或 NetMeeting 或适用于 Mac OSX 的 XMeeting）对个别研究人员进行视频会议访问。 其中许多解决方案都是开源的，仅需要用户级别的摄像头和麦克风以及机构级别的足够带宽。 此外，我们计划扩大合作实验室的使用，使研究人员能够使用位于核心仪器中心的高端仪器。 DBI 生物成像中心已在其多光子和场发射扫描电子显微镜上使用 Quartz PCI 协作软件，为全州的研究人员提供对这些独特而复杂的仪器的远程访问。