WORKSHOP AND TRAINING ACTIVITIES

研讨会和培训活动

• 批准号: 8170700
• 负责人: RICHARD D SMITH
• 金额: $ 3.32万
• 依托单位: BATTELLE PACIFIC NORTHWEST LABORATORIES
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8170700
• 关键词: Algorithms; Alzheimer' s Disease; American; Apple; Area; Arts; Awareness; Belgium; Biochemical; Biology; Biomedical Research; Biomedical Technology; Boxing; Brain; Breast Cancer Cell; California; Cell Fractionation; Cell physiology; Cellular biology; Collaborations; Communities; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Data; Data Analyses; Data Set; Diabetes Mellitus; Disease model; District of Columbia; Educational workshop; Environment; Evolution; Experimental Designs; Explosion; Fostering; Foundations; Fractionation; Funding; Future; Genomics; Goals; Grant; HIV Infections; Hepatic; Human; Image; Individual; Informatics; Institutes; Institution; International; Investigation; Islet Cell; Islets of Langerhans; Kidney Transplantation; Korea; Koreans; Laboratories; Length; Link; Liquid Chromatography; Liquid substance; Longevity; Lyme Disease; Malignant neoplasm of prostate; Mass Spectrum Analysis; Measurement; Membrane Microdomains; Metabolism; Methodology; Methods; Modeling; Mus; National Center for Research Resources; Nature; Netherlands; Neurites; North Carolina; Oranges; Oregon; Oxidative Stress; Pattern; Peer Review; Peptides; Phosphoric Monoester Hydrolases; Post-Translational Protein Processing; Progress Reports; Proteins; Proteome; Proteomics; Publications; Regulation; Reporting; Research; Research Personnel; Research Project Grants; Research Training; Resolution; Resources; Rest; Sampling; San Francisco; Science; Scientist; Signal Transduction; Signal Transduction Pathway; Societies; Software Tools; Solid; Solutions; Source; Stable Isotope Labeling; Subgroup; System; Systems Biology; Technology; Texas; Tissues; Training; Training Activity; Trees; Trust; United States National Institutes of Health; Universities; Urine; Visit; Washington; Work; abstracting; base; cancer cell; cell growth; comparative; design; forest; improved; interest; macrophage; meetings; new technology; novel strategies; open source; programs; protein complex; relating to nervous system; research study; response; software development; 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. 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. 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. 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. The 15 people in attendance each received a data disk (DVD) with the software installers for proteomics software developed at the Center, plus the example data used to prepare the presentation. 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. The ~35 people in attendance received a data disk (DVD) with the software installers for proteomics software developed at PNNL, plus the example data used to prepare the figures shown in the presentation. 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. These topics were aimed at getting increased information content from LC-MS experiments both within customized and commercially available LC-MS systems. A number of informatics tools and algorithms were described, many of which are either open-source or freely available at the NCRR website. A DVD was also distributed to attendees with software installers and demo data. 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. This subgroup brought together investigators with an interest and expertise in managing and analyzing large, heterogeneous datasets with the intent of building systems-level models of cellular functions. The state of the art was discussed and possibilities for community collaborations outlined. 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. The intent was to discuss the different approaches that are being used, the limitations and advantages of different solutions and where to find help. There will be three areas of discussion: 1) starting with good data, 2) linking data sets, 3) how to find patterns in the data. Both commercial and open source software packages will be discussed, although the emphasis will be on the latter, in particular CCE and Cytoscape. 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. This workshop brought together some of the preeminent individuals working in these areas in an interactive environment to both present their findings and discuss the implications and future directions of these important issues. 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. This tutorial will focus on the application of quantitative proteomic strategies (stable isotope labeling and absolute quantitation) in combination with recently developed sample fractionation and enrichment methodologies, including automated protein complex isolation and cell fractionation. The tutorial will include a presentation of the analysis methods for interpreting quantitative proteomics data and their application to analyzing cellular responses to exogenous stimulation. 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. Research Impact on Biomedical Research and Research Training The challenging collaborative research projects in progress at the PNNL Research Center cover a broad range of biomedical topics important to the community that the Center serves as well as stimulating increased awareness and interest in biomedical research at PNNL. Currently, the Center has subprojects situated with institutes in Belgium, and the Netherlands. The remaining subprojects are situated throughout the U.S.A. from coast to coast. The biomedical importance of this network of collaborative research projects includes the following topics: the investigation of signal transduction pathways and the associated phosphoproteome for quantitative modeling; the characterization of the phosphoproteome of cancer cell lamellipodia; neurite extension and retraction; the urine proteome and kidney transplantation; neural tissue signal transduction and its regulation by a specific phosphatase; CSF and Lyme disease; breast cancer cell enzymatics; the comparative 3D quantitative proteomic profiles of normal and disease model mouse brains; the quantitative proteomics profiling of normal human CSF and CSF from diseased subjects; characterization of pancreatic islet cell growth; prostate cancer; Alzheimer's Disease; enzymatic phosphatase activity in neuroproteomics; CSF proteomics in HIV infection; regulation of hepatic metabolism; the characterization of PTMs in the chromosomal passenger complex; the investigation of post-translational protein modifications related to oxidative stress; the extension of life span; alterations in macrophage lipid raft proteomics; and research on diabetes. Research training has been provided to both new postdoctoral researchers at the Research Center and scientists visiting the Center. Collaborative researchers from laboratories located in California, Texas, Oregon, and Washington visited the Center during this reporting period and received information and/or training. In addition, visiting scientists from institutes located in North Carolina, Texas, Korean University, Seoul National University, and University of Korea have visited the Center during this reporting period for various extended lengths. These visits provide an opportunity to educate other investigators and laboratories on the use of advanced proteomics technologies and the broader national and international research communities on the potential applications of proteome analysis technologies in biomedical and biochemical research.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 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。 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。 出席会议的15个人每个人都收到了一个数据磁盘（DVD），其中包括在中心开发的蛋白质组学软件的软件安装程序，以及用于准备演示文稿的示例数据。 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。 约35人出席的人收到了一个数据磁盘（DVD），其中包括PNNL开发的蛋白质组学软件的软件安装程序，以及用于准备演示文稿中显示的数字的示例数据。 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。 这些主题旨在从自定义和市售LC-MS系统中的LC-MS实验中获得增加信息内容。 描述了许多信息学工具和算法，其中许多是开源的或在NCRR网站上免费获得的。 还通过软件安装程序和演示数据将DVD分发给与会者。 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。 该亚组汇集了具有兴趣和专业知识的研究人员，以管理和分析大型，异质的数据集，其目的是建筑系统级别的蜂窝功能模型。 讨论了艺术的状态以及概述的社区合作的可能性。 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。 目的是讨论所使用的不同方法，不同解决方案的局限性和优势以及在哪里找到帮助。 将有三个讨论领域：1）从良好的数据开始，2）链接数据集，3）如何在数据中找到模式。 尽管重点将放在后者，特别是CCE和Cytoscape上，但将讨论商业和开源软件软件包。 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。 该研讨会汇集了在互动环境中在这些领域工作的一些杰出个人，以介绍他们的发现，并讨论这些重要问题的含义和未来方向。 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。 本教程将重点介绍定量蛋白质组学策略（稳定的同位素标记和绝对定量）以及最近开发的样品分馏和富集方法，包括自动化蛋白质复合物分离和细胞分馏。 该教程将包括用于解释定量蛋白质组学数据的分析方法及其在分析细胞对外源刺激反应的应用。 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。 研究对生物医学研究和研究培训的影响 PNNL研究中心正在进行的具有挑战性的合作研究项目涵盖了对社区至关重要的广泛的生物医学主题，这些主题以及刺激PNNL生物医学研究的意识和兴趣的提高。 目前，该中心在比利时和荷兰的机构中设有副投射。 其余的次要投影位于整个美国从海岸到海岸。 该协作研究项目网络的生物医学重要性包括以下主题：信号转导途径的研究和相关的磷蛋白酶用于定量建模；癌细胞层状脂蛋白磷酸蛋白酶的表征；神经突的延伸和缩回；尿液蛋白质组和肾脏移植；神经组织信号转导及其对特定磷酸酶的调节； CSF和莱姆病；乳腺癌细胞酶学；正常和疾病模型小鼠大脑的比较3D定量蛋白质组学特征；正常人CSF和CSF的定量蛋白质组学分析来自患病受试者；胰岛细胞生长的表征；前列腺癌；阿尔茨海默氏病；神经蛋白质组学中的酶促磷酸酶活性； HIV感染中的CSF蛋白质组学；调节肝代谢；染色体乘客复合物中PTM的表征；与氧化应激有关的翻译后蛋白质修饰的研究；寿命的延长；巨噬细胞脂质筏蛋白质组学的改变；和糖尿病的研究。 已经向研究中心的新博士后研究人员和参观该中心的科学家提供了研究培训。 来自位于加利福尼亚州，得克萨斯州，俄勒冈州和华盛顿的实验室的合作研究人员在此报告期间参观了该中心，并接受了信息和/或培训。 此外，来自位于北卡罗来纳州，得克萨斯州，韩国大学，首尔国立大学和韩国大学的学院的科学家在此报告期间访问了该中心。 这些访问为其他研究人员和实验室提供了一个机会，以了解先进蛋白质组学技术的使用以及更广泛的国家和国际研究社区，以了解蛋白质组分析技术在生物医学和生化研究中的潜在应用。