VERMONT INBRE: BIOINFORMATICS CORE

佛蒙特州因布雷：生物信息学核心

• 批准号: 7381408
• 负责人: JEFFREY P. BOND
• 金额: $ 20.74万
• 依托单位: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2007-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7381408
• 关键词: VERMONT; INBRE; BIOINFORMATICS; CORE

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 2005 ¿ June 30, 2006 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. Highlights Support for oligonucleotide arrays (Affymetrix GeneChips) continues to be productive (Table) and to occupy Dr. Anjanette Watson full time. Highlights include ¿ two peer-reviewed publications from support activities since September 2005, ¿ support for an NIH R01 at Middlebury College, ¿ two studies (a total of 82 GeneChips) on human biopsies, ¿ strong support for bovine researchers (four projects) in the College of Agriculture and Life Sciences at UVM, ¿ support for experiment design, including analysis of sources of variation and power calculations based on publicly available data. We provided designs for 9 projects that have not yet begun. Project Area Organism Source Chips Project Status Cardiovascular Disease Human Cell culture 8 Peer reviewed publication Milk production Mouse Mammary surgery 8 Peer reviewed manuscript Dental caries Strep. Mutans WT/KO culture 15 Manuscripts in preparation. Milk production Cow Mammary biopsy 8 Manuscript in preparation Cardiovascular Disease Rat Brain surgery 6 Manuscript in preparation Immune Response Mouse Primary Culture 6 Inferences validated by RTQ-PCR. Muscle atrophy Human Muscle biopsy 15 RTQ-PCR Validation of inferences in progress Milk production Cow Mammary biopsy 8 Validation in process Breast Cancer Human Breast biopsy 67 Analysis in process: Significant inferences based on permutation test. Connective Tissue Remodeling Mouse Plexus surgery 6 Analysis in progress Brain function Mouse Brain surgery 8 Analysis in process Radiation Damage Human Cell culture 4 Outreach/Educ Yeast Culture 20 Completed modules at 4 colleges TOTAL 6 179 2 peer-reviewed manuscripts Table: Affymetrix GeneChip studies processed by the BC during Sep 2005 ¿ June 2006. AIM 2 Provide laboratory/lecture modules to Baccalaureate Institutions (BPI). The BC played a role in the highly successful VGN oligonucleotide microarray outreach module, a BioQuest BEDROCK bioinformatics workshop, and guest lectures on NCBI resources. In collaboration with the Outreach Core we will deliver laboratory/lecture modules involving gene expression, proteomics, and bioinformatics. Microarray outreach activities are described in the Outreach Core progress report. In addition: ¿ Dr. William Barnes, on sabbatical with the VGN from Clarion University in Pennsylvania, developed a bioinformatics outreach module and is in the process of gathering feedback at UVM. ¿ VGN staff, Dr. Anjanette Watson and Bryan Fleming, hosted a three day NCBI workshop. The VGN ERIS resource (see Aim 3) was used to announce the workshop statewide and attendance was at capacity (80 people on the first day and 40 on the two subsequent days). Attendees represented Norwich University, Green Mountain College, and the Rat Genome Database, as well as 11 departments/units (4 colleges) at UVM. AIM 3 Support the development of administrative infrastructure for electronic networks (Figure 2). With BRIN funding the BC developed infrastructure that allows organizations to monitor changing needs, interests, and progress of participants, to collect usage data, to target information to participants, and to match advisors with prot¿g¿s. This support is based on ¿member profiles¿. Such infrastructure is already in use; proposed activities would allow us to share it with both other Vermont organizations and with other INBRE awardees. 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. ERIS resources have been used to make 11 statewide announcements and to capture the publications and keyword indexing of 25 UVM scientists. Briefly, the idea underlying ERIS is to take advantage of publicly available 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.

该主题是使用NIH/NCRR资助的中心赠款提供的资源的众多研究主题之一。主题和研究人员（PI）可能已经从另一名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。列出的机构是针对该中心的，这不是调查人员的机构。佛蒙特州遗传学网络生物信息学核心（BC）2005年9月30日，2006年6月30日，针对BC的三个目标，我们重印了目标，然后摘要亮点。 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。突出显示了对寡核苷酸阵列（Affymetrix Genechips）的支持（表格），并全职占领Anjanette Watson博士。亮点包括“自2005年9月以来的支持活动中的两份同行评审出版物，»对米德尔伯里学院的NIH R01的支持，两项研究（总共82个巨头）对人类活检，强烈支持牛牛研究人员（四个项目）在UVM上进行了对UVM的启动及其对UVM的启示的启示，commutional compuitions contimutions？ 数据。我们为尚未开始的9个项目提供了设计。项目区组织源芯片项目状态心血管疾病人类细胞培养8同行评审出版牛奶生产小鼠乳腺手术8同行手稿龋齿链球菌。 Mutans WT/KO培养15手稿准备。牛奶生产牛乳腺活检8制备中的手稿心血管疾病大鼠脑外科手术6手稿在制备免疫反应小鼠原发性培养物6推理RTQ-PCR验证的推论。肌肉萎缩人类肌肉活检15 RTQ-PCR验证牛奶生产的推论奶牛乳腺活检8过程中的乳腺癌验证乳腺癌人类乳房活检67过程中的分析：基于固定测试的重要信息。结缔组织重塑小鼠丛集手术6分析脑功能的分析脑功能小鼠脑外科手术8分析损害人类细胞培养4外展/教育酵母菌培养20在4所大学中完成的模块总数6 179 2同行评审手稿表：Affymetrix Genechip研究由BC 2005年6月2005年的BACERET进行了2006年6月2日。 （BPI）。卑诗省在非常成功的VGN寡核苷酸微阵列外展模块中发挥了作用，生物Quest Bedrock生物信息学研讨会以及有关NCBI资源的来宾演讲。通过与外展核心合作，我们将提供涉及基因表达，蛋白质组学和生物信息学的实验室/讲座模块。微阵列外展活动在《外展核心进度报告》中描述。此外：�威廉·巴恩斯（William Barnes）博士在宾夕法尼亚州克拉里昂大学（Clarion University）的VGN休假，开发了生物信息学外展模块，并正在UVM收集反馈。 VGN的工作人员Anjanette Watson博士和Bryan Fleming举办了为期三天的NCBI研讨会。 VGN Eris资源（请参阅AIM 3）用于宣布全州的研讨会，出席人数为（第一天80人，随后的两天40人）。与会者代表诺里奇大学，绿山学院和大鼠基因组数据库，以及UVM的11个部门/单位（4个大学）。 AIM 3支持电子网络行政基础设施的开发（图2）。借助BRIN资金，卑诗省开发了基础架构，使组织能够监视参与者的需求，兴趣和进步，以收集使用数据，将信息定位为参与者，并与Prot` g s一起匹配顾问。此支持基于„成员资料。这种基础架构已经在使用；拟议的活动将使我们能够与其他佛蒙特州组织和其他近亲获奖者分享。 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。 ERIS资源已被用来发表11份全州公告，并捕获25位UVM科学家的出版物和关键字索引。简而言之，ERIS的基础想法是利用公共个人目录，书目引用数据库，授予奖励数据库和日历中的公开信息，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。