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.

该子项目是利用 NIH/NCRR 资助的中心拨款提供的资源的众多研究子项目之一，该子项目和研究者 (PI) 可能已从其他 NIH 来源获得主要资助，因此可以在其他 CRISP 机构中得到体现。列出的是该中心，该中心不一定是研究者所在的机构 佛蒙特州遗传学网络生物信息学核心 (BC) 2005 年 9 月亮点 ¿ 2006 年 6 月 30 日 对于三个 BC 目标，我们转载了目标，然后总结了要点 1 提供生物信息学服务，使研究人员在研究资助方面更具竞争力。这些服务将包括。支持程序实验寡核苷酸微阵列、LC-质谱和蛋白质结构/功能更一般地，BC 支持定制数据库的开发。 (Affymetrix GeneChips) 继续保持高效（表）并全职占用 Anjanette Watson 博士，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，¿两项关于人体活检的研究（总共 82 个基因芯片），¿为 UVM 农业与生命科学学院的牛研究人员（四个项目）提供大力支持，¿支持实验设计，包括基于公开数据的变异来源分析和功效计算 我们为尚未开始的 9 个项目提供了设计。 项目领域 生物源芯片 项目状态 心血管疾病 人类细胞培养 8 同行评审出版物 牛奶生产。小鼠乳腺手术 8 同行评审手稿 龋齿链球菌 WT/KO 培养物 15 手稿正在准备 牛奶生产 牛乳腺活检 8 手稿正在准备 心血管疾病 大鼠脑部手术6 准备中的手稿 免疫反应 小鼠原代培养物 6 通过 RTQ-PCR 验证的推论 人类肌肉活检 15 RTQ-PCR 正在进行的推论验证 产奶量 牛乳腺活检 8 正在进行中的验证 乳腺癌 人类乳房活检 67 正在进行中的分析：基于结缔组织重塑小鼠丛手术的重要推论 6 正在进行的脑功能分析小鼠脑部手术 8 正在进行的分析 辐射损伤 人类细胞培养 4 Outreach/Educ 酵母培养 20 在 4 所学院完成的模块 总计 6 179 2 份同行评审手稿 表：BC 在 2005 年 9 月期间处理的 Affymetrix GeneChip 研究 ¿ 2006 年 6 月。 AIM 2 向学士学位机构 (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 生物信息学研讨会以及与外展资源合作的客座讲座中发挥了作用。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/讲座模块的核心，在外展核心进展中进行了描述。另外： ¿ William Barnes 博士在宾夕法尼亚州克拉里昂大学 VGN 休假期间开发了一个生物信息学外展模块，目前正在 UVM 收集反馈。 VGN 工作人员 Anjanette Watson 博士和 Bryan Fleming 主持了为期三天的 NCBI 研讨会，VGN ERIS 资源（参见目标 3）用于宣布研讨会被告，出席人数已满（第一天 80 人，第二天 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 个系/单位（4 个学院）。 3 支持电子管理基础设施的发展。在 BRIN 的资助下，BC 开发了基础设施，使组织能够监控参与者不断变化的需求、兴趣和进度，收集使用数据，向参与者提供目标信息，并将顾问与利益相匹配。克此支持基于 ¿会员简介¿此类基础设施已投入使用；拟议的活动将使我们能够与其他佛蒙特州组织和其他 INBRE 获奖者共享该基础设施，该数据库已开始建设佛蒙特州科学技术专家数据库。 VGN ERIS 项目。ERIS 资源已用于发布 11 个全州范围的公告，并获取 25 名 UVM 科学家的出版物和关键词索引。 简而言之，ERIS 的基本理念是利用公共人事名录中的公开信息。书目引文数据库、资助奖项数据库和日历，以提供有关人员的信息？这些信息将通过联邦电子邮件公告、网页和自动通知参与者新条目的机器人进行交换。