WORKSHOP AND TRAINING ACTIVITIES

研讨会和培训活动

• 批准号: 8365463
• 负责人: RICHARD D SMITH
• 金额: $ 5.18万
• 依托单位: BATTELLE PACIFIC NORTHWEST LABORATORIES
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8365463
• 关键词: American; Apple; Area; Awareness; Biology; Biomedical Technology; Boxing; Cell physiology; Cellular biology; Collaborations; Communities; Complex; Computer software; Data; Data Analyses; Data Set; District of Columbia; Educational workshop; Evolution; Experimental Designs; Explosion; Fostering; Foundations; Funding; Genomics; Goals; Grant; Image; Informatics; Institution; Liquid Chromatography; Liquid substance; Mass Spectrum Analysis; Measurement; National Center for Research Resources; Nature; Oranges; Peer Review; Peptides; Principal Investigator; Progress Reports; Proteins; Proteome; Proteomics; Publications; Research; Research Infrastructure; Research Personnel; Resolution; Resources; Rest; Sampling; San Francisco; Science; Scientist; Societies; Software Tools; Solid; Source; Subgroup; Systems Biology; Technology; Training Activity; Trees; Trust; United States National Institutes of Health; abstracting; base; cost; design; experimental analysis; forest; improved; interest; meetings; new technology; novel strategies; open source; programs; research study; sound; stem; symposium; tool; tool development; web site

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Accessibility of advanced proteomics technologies to the biomedical community is a longer-term goal of the Research Center. This information transfer is made possible by the NCRR website (full details on website on page 26 of the Research Progress Report) and the hosting of workshops and tutorials. Since the establishment of our NCRR program, the Center has organized two NCRR workshops and participated in six short courses/tutorials. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in San Diego, CA in February 2009. This is the third consecutive year that the PNNL NCRR informatics team has presented this invited course. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including an overview of quantitative approaches and software tools available to the community, considerations for experimental design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in Bethesda, MD in March 2008. The course covered several aspects of quantitative proteomics using LC-MS analysis platforms, including a comparison of the approaches and software tools available to the community, considerations for experiment design, feature discovery in LC-MS datasets, and statistically sound analysis of identified peptides and proteins. These topics were aimed at informing researchers about the issues to consider when designing LC-MS experiments, while also describing the general approaches used for extracting information content from LC-MS data. A Short Course titled, "Data Extraction and Analysis for LC-MS Based Proteomics" was given at the U.S. HUPO meeting in Seattle, WA in March 2007. The course was intended to educate the U.S. proteomics community and discuss the use of two different LC-MS data extraction and analysis platforms to demonstrate how high mass measurement accuracy mass spectrometry and high resolution liquid chromatography could be applied for higher-throughput proteomics. The topics presented include 1) LC-MS feature extraction, 2) experimental design and analysis of large LC-MS datasets, and 3) identification and characterization of peptides and proteins using LC-MS. A Special Interest Subgroup titled, "Managing the Data Explosion in Systems Biology" was held at the American Society for Cell Biology (ASCB) Meeting in San Diego, CA in December 2006. The following abstract summarizes the Special Interest Subgroup at the ASCB meeting entitled: New technologies in genomics, proteomics, and quantitative imaging are producing enormous amounts of data that promise to revolutionize biology in the upcoming decades. To realize this potential, however, new approaches must be developed to manipulate, integrate and analyze the large datasets that these technologies can generate. Otherwise, the trees will continue to obscure the forest. A Tutorial titled, "Apples and Oranges: Integrating Disparate Data Sets to Understand Complex Cellular Function" was presented at the American Society for Cell Biology (ASCB) Meeting in San Francisco, CA in December 2005. The following abstract summarizes the tutorial presentation: Systems biology requires the integration of many types of data to understand complex cell processes. Unfortunately, it is currently very difficult to connect disparate data sets. This tutorial provided an overview of software-based approaches to handle heterogeneous data sets, such as proteomics and microarray data. A NCRR Workshop titled, "Separations and Mass Spectrometry Applied to Proteomics and the Informatics Challenges" was planned and executed at PNNL in conjunction with a Proteome Society Meeting hosted by PNNL in April 2005. The following is a description that emphasizes the focus of the workshop: Among the issues confronting the proteomics community, few may be as important as those covered in this workshop. Specifically, we covered both data dissemination standards as well as open source software tools that help analyze that data. Data standards are vital to the growing collaborative nature of large scale proteomics studies in that they will allow multiple institutions located in diverse areas to share the results of instrumental analyses without the requirement that many separate analysis software tools be broadly distributed amongst those groups. Further, standardized formats will simplify publication of analyzed data, fostering rigorous peer review of results and new analysis tool development. Indeed, open source data analysis tool development, wherein the software that enables discovery science as applied to proteomics becomes available to all institutions for use and improvement, was the second major issue covered during the workshop. Rather than requiring collaborators to simply trust the results that stem from black-box style analysis tools, open source software allows any institution to examine, validate, and ultimately, improve these tools when and where appropriate. Lastly, open source tools provide a more solid foundation upon which exciting discoveries may rest. A Tutorial titled, "Mass Spectrometry-based Quantitative Proteomics for Cell Biology" was presented at the American Society for Cell Biology (ASCB) Meeting in Washington D.C. in December 2004. The following abstract summarizes the tutorial presentation: The effective integration of proteomics data into cell biology studies requires both identification and quantification of the proteins. Mass spectrometry combined with high-resolution liquid chromatographic separations of fractionated or enriched peptide samples represents a highly efficient approach to peptide identification and quantitation. A NCRR Proteomics Workshop titled, "Quantitative Proteomics Applied to Cellular Function" was held in conjunction with the 2004 Northwest Symposium for Systems Biology at PNNL in June 2004. The focus of the workshop was on the evolution of quantitative proteomics. The goals of the workshop were (1) to educate researchers to the utility of the application of quantitative proteomics to understanding cellular function; (2) to stimulate possible new collaborations between the presenters, participating scientists, and the Research Center; and (3) to increase the awareness of the scientific community to the NCRR Biomedical Technology Research Center at PNNL.

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。对该子项目的主要支持和子弹的主要研究者可能由其他来源（包括其他NIH来源）提供。 该子项目列出的总成本可能代表了子项目使用的估计中心基础设施的估计数量，而不是NCRR赠款向子项目或副标理人员提供的直接资金。 先进的蛋白质组学技术对生物医学界的可访问性是研究中心的长期目标。 NCRR网站（研究进度报告的第26页的网站上的完整详细信息）和讲习班和教程的托管使此信息传输成为可能。 自成立NCRR计划以来，该中心已经组织了两个NCRR研讨会，并参加了六个简短的课程/教程。 在2009年2月在美国加利福尼亚州圣地亚哥举行的美国HUPO会议上，给了一门标题为“基于LC-MS的蛋白质组学的数据提取和分析”的简短课程。 这是PNNL NCRR信息学团队连续第三年提出了这一受邀课程。 该课程使用LC-MS分析平台介绍了定量蛋白质组学的几个方面，包括社区可用的定量方法和软件工具的概述，实验设计的考虑，LC-MS数据集中的特征发现以及对已识别肽和蛋白质的统计良好分析。 在2008年3月在马里兰州贝塞斯达举行的美国HUPO会议上，给了一门标题为“基于LC-MS的蛋白质组学的数据提取和分析”。 该课程使用LC-MS分析平台涵盖了定量蛋白质组学的几个方面，包括对社区可用的方法和软件工具的比较，实验设计的考虑，LC-MS数据集中的特征发现以及对已识别肽和蛋白质的统计良好分析。 这些主题旨在向研究人员告知设计LC-MS实验时要考虑的问题，同时还描述了用于从LC-MS数据中提取信息内容的一般方法。 在2007年3月在华盛顿州西雅图的美国HUPO会议上，给了一门标题为“基于LC-MS的蛋白质组学的数据提取和分析”的简短课程。 该课程旨在教育美国蛋白质组学界，并讨论使用两个不同的LC-MS数据提取和分析平台的使用，以证明如何将高质量测量精度质谱和高分辨率液相色谱法应用于高通量蛋白质组学。 提出的主题包括1）LC-MS特征提取，2）大型LC-MS数据集的实验设计和分析，以及3）使用LC-MS识别和表征肽和蛋白质。 2006年12月，在美国加利福尼亚州圣地亚哥举行的美国细胞生物学学会（ASCB）会议上举行了一个特殊的兴趣亚组，标题为“管理系统生物学中的数据爆炸”。 以下摘要总结了ASCB会议上的特殊兴趣子组，标题为：基因组学，蛋白质组学和定量成像的新技术正在产生大量数据，这些数据有望在接下来的几十年中彻底改变生物学。 但是，要意识到这种潜力，必须开发出新的方法来操纵，整合和分析这些技术可以生成的大型数据集。 否则，树木将继续掩盖森林。 2005年12月在加利福尼亚州旧金山举行的美国细胞生物学学会（ASCB）会议上，介绍了一项名为“苹果和橘子：整合不同数据集以了解复杂细胞功能”的教程。 以下摘要总结了教程演示：系统生物学要求将许多类型的数据集成以了解复杂的细胞过程。 不幸的是，目前很难连接不同的数据集。 本教程提供了基于软件的方法来处理异质数据集的概述，例如蛋白质组学和微阵列数据。 NCRR研讨会标题为“应用于蛋白质组学的分离和质谱法和信息学挑战”是在PNNL和2005年4月由PNNL举办的蛋白质组社会会议上进行的。 以下是强调研讨会重点的描述：在蛋白质组学社区面临的问题中，很少有人比本研讨会中涵盖的问题那么重要。 具体来说，我们涵盖了两个数据传播标准以及有助于分析数据的开源软件工具。 数据标准对于大规模蛋白质组学研究的不断增长的协作性质至关重要，因为它们将允许位于不同领域的多个机构共享仪器分析的结果，而无需要求许多单独的分析软件工具在这些组之间进行广泛分配。 此外，标准化格式将简化分析数据的发表，从而促进对结果的严格同行评估和新的分析工具开发。 实际上，开源数据分析工具开发（其中启用适用于蛋白质组学的发现科学的软件都可以用于所有机构的使用和改进，这是研讨会期间的第二个主要问题。 开源软件并没有要求合作者简单地相信源于黑框样式分析工具的结果，而是允许任何机构在适当的情况下检查，验证并最终改善这些工具。 最后，开源工具为令人兴奋的发现提供了更坚实的基础。 2004年12月在华盛顿特区举行的美国细胞生物学学会（ASCB）会议上，介绍了一项名为“基于质谱的定量蛋白质组学”的教程。 以下摘要总结了教程介绍：将蛋白质组学数据与细胞生物学研究的有效整合需要鉴定和定量蛋白质。 质谱法与分离或富集的肽样品的高分辨率液相色谱分离结合在一起，代表了一种高效的肽鉴定和定量方法。 NCRR蛋白质组学研讨会，标题为“应用于细胞功能的定量蛋白质组学”，并与2004年6月在PNNL的2004年西北系统生物学研讨会结合了2004年6月。 研讨会的重点是定量蛋白质组学的演变。 研讨会的目标是（1）教育研究人员，以应用定量蛋白质组学在理解细胞功能方面的应用； （2）刺激演示者，参与科学家和研究中心之间可能的新合作； （3）提高科学界对PNNL NCRR生物医学技术研究中心的认识。