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.

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。佛蒙特遗传网络生物信息学核心（BC）亮点2005年9月至2006年6月30日对于三个BC目标中的每一个，我们都重印了目标，然后总结了亮点。目标1：提供生物信息学服务，使研究人员在获得研究经费方面更具竞争力。服务包括实验设计以及数据管理和分析。这些服务将包括支持涉及寡核苷酸微阵列、lc -质谱和蛋白质结构/功能的实验项目。更一般地说，BC支持定制数据库的开发。支持寡核苷酸阵列（Affymetrix基因芯片）继续生产（表），并占用博士Anjanette Watson全职。亮点包括自2005年9月以来支持活动的两份同行评审出版物，对米德尔伯里学院NIH R01的支持，对人类活组织检查的两项研究（总共82个基因芯片），对UVM农业和生命科学学院牛研究人员（四个项目）的大力支持，对实验设计的支持，包括对变异源的分析和基于公开数据的功率计算。我们提供了9个尚未开始的项目的设计。项目领域生物来源芯片项目现状心血管疾病人类细胞培养8同行评议出版物产奶小鼠乳腺外科8同行评议手稿龋齿链球菌Mutans WT/KO培养15份手稿正在准备中。产奶奶牛乳腺活检8准备稿心血管疾病大鼠脑外科6准备稿免疫反应小鼠原代培养6 RTQ-PCR验证的推论。肌肉萎缩人类肌肉活检15 RTQ-PCR正在进行的推断验证产奶奶牛乳腺活检8正在进行的验证乳腺癌人类乳房活检67正在进行的分析：基于排列试验的显著推断。结缔组织重塑小鼠神经丛手术6进行中分析脑功能小鼠脑手术8过程中分析辐射损伤人类细胞培养4外展/教育酵母培养20在4所学院完成模块总数6 179 2同行评议手稿表：2005年9月至2006年6月期间BC处理的Affymetrix基因芯片研究。目标2：为学士学位院校（BPI）提供实验室/讲座模块。BC在非常成功的VGN寡核苷酸微阵列外展模块、BioQuest BEDROCK生物信息学研讨会和NCBI资源客座讲座中发挥了重要作用。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进行了描述。此外：威廉·巴恩斯博士在宾夕法尼亚州克莱里昂大学的VGN休假期间，开发了一个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主持了一个为期三天的NCBI研讨会。VGN ERIS资源（见目标3）用于宣布全州范围内的研讨会，与会人数达到上限（第一天80人，随后两天40人）。与会者代表了诺威奇大学、绿山学院和大鼠基因组数据库，以及弗吉尼亚大学11个系/单位（4个学院）。目标3支持电子网络管理基础设施的发展（图2）。在BRIN的资助下，BC开发了基础设施，使组织能够监控不断变化的需求、兴趣和参与者的进展，收集使用数据，向参与者提供目标信息，并将顾问与项目相匹配。这种支持是基于“成员档案”。这样的基础设施已经在使用；拟议的活动将使我们能够与佛蒙特州的其他组织和其他INBRE获奖者分享。VGN启动了佛蒙特州科学技术专家数据库的建设，该数据库的范围逐渐扩大，成为VGN ERIS项目。ERIS资源已被用于发布11个全州范围的公告，并捕获了25位UVM科学家的出版物和关键词索引。简而言之，ERIS的基本思想是利用公共人事目录、书目引文数据库、拨款奖励数据库和日历中的公开信息，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。这些信息将通过全州范围内的电子邮件公告、网页和自动通知参与者新条目的机器人来交换。