VERMONT INBRE: BIOINFORMATICS CORE

佛蒙特州因布雷：生物信息学核心

基本信息

批准号：
7610033
负责人：
JEFFREY P. BOND
金额：
$ 25.76万
依托单位：
UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-07-01 至 2008-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7610033
关键词：
Award Bioinformatics Bos taurus Calendar Categories Cattle Centers of Research Excellence Clinical Research Computer Retrieval of Information on Scientific Projects Database Consult Custom Data Analyses Databases Development Directories Drosophila genus Electronic Mail Electronics Event Experimental Designs Facility Construction Funding Category Faculty Funding Genetic Genotype Grant Human Human Resources Immunobiology Individual Institution Internet Laboratories Mass Spectrum Analysis Medicine Mercury Numbers Oligonucleotide Microarrays Open Reading Frames Participant Pattern Phase I Clinical Trials Positioning Attribute Principal Investigator Process Publications Published Directory Regulation Reporting Research Research Infrastructure Research Personnel Research Project Grants Research Support Resources Robot Sampling Science Service Statistics Services Source Streptococcus mutans Technology Toxic effect Toxoplasma gondii United States National Institutes of Health Vermont base college data management interest lectures malignant breast neoplasm member novel outreach programs protein structure function success

项目摘要

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. Vermont Genetics Network Bioinformatics Core (BC) Highlights September 2006 April 11, 2007 For each of the three BC Aims we reprint the aim and then summarize highlights. AIM 1 Provide bioinformatics services that make investigators more competitive for research funding. Services include experimental design as well as data management and analysis. These services will include support for experimental programs involving oligonucleotide microarrays, LC-Mass spectrometry, and protein structure/function. More generally, the BC supports development of custom databases. Bioinformatics Core services have emphasized microarray data analysis because of the overwhelming success of the VGN Microarray Facility. The VGN supported a microarray data analysis position with INBRE funds, a position that has now moved largely to a combination of College of Medicine support and federal research grants to individual investigators. Thus we used INBRE funds to add a microarray data analysis position that subsequently moved to self-sustainability. Highlights: + The microarray user 24 NIH-funded investigators (FY2006), 17 departments of UVM, and a high proportion of junior investigators (Table 1). About half of the services support human expression or genotype analysis (bottom table) but these facilities also support special interests such as Bos Taurus, Streptococcus mutans, and Toxoplasma gondii research. + Support for an NIH R01 grant to an investigator (Grace Spatafora) at Middlebury College. In addition to calculation of expression statistics, services included identification of co-regulation based on correlated expression patterns, and identification of novel open reading frames. Five Middlebury College undergraduates participated in this research. + A new BCRF grant to Dr. Hyman Muss for microarray studies on human breast cancer samples. + A USDA grant to Dr. Thomas McFadden for bovine microarray studies. + An NIH R01 grant to Dr. Matthew Rand for GeneChip studies of methyl mercury toxicity. + A COBRE award to Dr. Ralph Budd for immunobiology research that includes GeneChip studies. Three of the investigators participating in this COBRE use microarray in their research. + Support for a junior faculty member, Dr. Giselle Sholler, involved in clinical research that includes a Phase I clinical trial of a neuroblatoma therapy. AIM 2 Provide laboratory/lecture modules to Baccalaureate Institutions (BPI). The Bioinformatics Core provided some consulting services to Dr. Janet Murray, VGN Outreach coordinator, during ongoing development of her Bioinformatics and Microarray modules. However, that Dr. Murray is now functioning exceptionally well independently so the Outreach Core deserves full credit for the success of Bioinformatics and Microarray Outreach Modules. AIM 3 Support the development of administrative infrastructure for electronic networks. The VGN initiated construction of a database of Vermont Experts in Science and Technology, which has since grown in scope to become the VGN ERIS Project. Briefly, the idea underlying ERIS is to take advantage of information in public personnel directories, bibliographic citation databases, grant award databases, and calendars to provide information about people's expertise and interests, research projects, publications, and events. This information will be exchanged through statewide email announcements, a web page, and robots that automatically notify participants of new entries. ERIS was used to make 13 statewide announcements during the reporting period. PI Category # Faculty members 41 NIH-funded, FY06 24 Junior faculty 13 Institutions 3 UVM Departments 17 Table 1. Principal Investigators (PI) on projects that involve microarrays. Chip Number ATH1-121501 27 Bovine 52 DrosGenome1 8 Drosophila_2 6 HG-U133A 123 HG-U133A_2 94 HG-U133_Plus_2 8 MG_U74Av2 34 MOE430A 34 Mapping250K_Nsp 34 Mapping250K_Sty 5 Mouse430A_2 38 Mouse430_2 6 Mu11KsubA 4 RAE230A 38 RG_U34A 19 S_mutans530155 17 Tgondiia520372 9 TOTAL 556 Table 2. Chips processed by the VGN Microarray Facility or by the VGN Bioinformatics Core

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。佛蒙特州遗传学网络生物信息学核心（BC）亮点 2006年9月2007年4月11日对于三个BC的目标，我们重印了目标，然后总结了亮点。 AIM 1提供生物信息学服务，使研究人员在研究资金方面更有竞争力。服务包括实验设计以及数据管理和分析。这些服务将包括对涉及寡核苷酸微阵列，LC-MAS光谱法和蛋白质结构/功能的实验程序的支持。更普遍地，卑诗省支持自定义数据库的开发。生物信息学核心服务强调了微阵列数据分析，因为VGN微阵列设施取得了压倒性的成功。 VGN用Inbre基金支持了微阵列数据分析职位，该职位现在已转化为医学院支持学院和联邦研究赠款的组合。因此，我们使用近亲资金添加了一个微阵列数据分析位置，随后将其转移到自我可持续性。亮点： +微阵列用户24名NIH资助的研究人员（2006财年），17个UVM部门和很大比例的初级调查人员（表1）。大约一半的服务支持人类的表达或基因型分析（底部表），但这些设施还支持特殊的兴趣，例如Bos Taurus，链球菌突变和Toxoplasma Gondii研究。 +支持在米德尔伯里学院（Middlebury College）向调查员（Grace Spatafora）提供NIH R01赠款。除了计算表达统计数据外，服务还包括基于相关表达模式的共同调节以及新颖的开放阅读框架的识别。五名米德尔伯里学院的本科生参加了这项研究。 + Hyman Muss博士的新BCRF授予了人类乳腺癌样品的微阵列研究。 +向托马斯·麦克法登（Thomas McFadden）博士提供牛微阵列研究的USDA赠款。 + NIH R01授予Matthew Rand博士的甲基汞毒性研究。 +包括Genechip研究在内的Ralph Budd博士授予的鞋垫奖。参与此鞋垫的三名研究人员在研究中使用微阵列。 +支持初级教师Giselle Sholler博士参与临床研究，其中包括一项I期临床试验。 AIM 2向学士学位机构（BPI）提供实验室/讲座模块。在她的生物信息学和微阵列模块的持续开发过程中，生物信息学核心为VGN外展协调员Janet Murray博士提供了一些咨询服务。但是，默里博士现在独立地运作异常出色，因此外展核心应为生物信息学和微阵列外展模块的成功而获得全部信誉。 AIM 3支持电子网络行政基础设施的开发。 VGN启动了佛蒙特州科学技术专家数据库的构建，此后在范围内发展成为VGN Eris项目。简而言之，ERIS的想法是利用公共人员目录中的信息，书目引用数据库，授予奖励数据库和日历，以提供有关人们的专业知识和兴趣，研究项目，出版物和事件的信息。此信息将通过全州范围的电子邮件公告，网页和机器人进行交换，这些机器人自动将新条目通知参与者。在报告期间，Eris被用来在全州范围内发布13个公告。 PI类别＃教师41 NIH资助，2006财年24 初级教师13 机构3 UVM部门17 表1。有关涉及微阵列的项目的主要研究人员（PI）。芯片编号 ATH1-121501 27 牛52 Drosgenome1 8 果蝇_2 6 HG-U133A 123 HG-U133A_2 94 HG-U133_PLUS_2 8 MG_U74AV2 34 MOE430a 34 Mapping250K_NSP 34 Mapping250K_Sty 5 鼠标430a_2 38 鼠标430_2 6 MU11KSUBA 4 RAE230a 38 RG_U34A 19 S_MUTANS530155 17 tgondiia520372 9 总计556 表2。由VGN微阵列设施或VGN生物信息学核心处理的芯片