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资助的中心赠款提供的资源的许多研究子项目之一。子项目和研究者（PI）可能从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。所列机构为中心，不一定是研究者所在机构。佛蒙特州遗传学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，我们重印目标，然后总结亮点。目标1提供生物信息学服务，使研究人员更有竞争力的研究资金。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-质谱和蛋白质结构/功能的实验项目的支持。更一般地，BC支持定制数据库的开发。 亮点对寡核苷酸阵列（AffysseGeneChips）的支持继续富有成效（表），并占据了Anjanette沃森博士的全部时间。亮点包括：自2005年9月以来，来自支持活动的两篇同行评审的出版物，支持米德尔伯里学院的NIH R 01，（共82个基因芯片）对人类活组织检查，对牛研究人员的有力支持（四个项目）在农业和生命科学学院在VM，支持实验设计，包括基于公开数据的变异源分析和功效计算。我们为9个尚未开始的项目提供了设计。 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房手术8同行评审手稿龋齿链球菌。突变体WT/KO培养物15份，制备中。牛奶生产奶牛乳房活检8准备中的Mannipt心血管疾病大鼠脑外科手术6准备中的Mannipt免疫反应小鼠原代培养6通过RTQ-PCR验证的推断。肌肉萎缩人类肌肉活检15 RTQ-PCR正在进行的推断验证牛奶生产奶牛乳房活检8正在进行的验证乳腺癌人类乳腺活检67正在进行的分析：基于排列检验的显著推断。结缔组织重塑小鼠神经丛手术6正在进行中的分析脑功能小鼠脑手术8正在进行中的分析辐射损伤人类细胞培养4外展/教育酵母培养20在4所大学完成的模块总计6 179 2同行评审的手稿表：2005年9月至2006年6月期间由BC处理的Affyestic基因芯片研究。 目标2：向学士学位机构提供实验室/讲座单元。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。微阵列外展活动见外展核心进展报告。此外还有：¿威廉巴恩斯博士，休假与VGN从克拉里昂大学在宾夕法尼亚州，开发了一个生物信息学外展模块，并在收集反馈的过程中在UVM。 VGN的工作人员Anjanette沃森博士和布赖恩弗莱明主持了为期三天的NCBI研讨会。VGN ERIS资源（见目标3）用于在全州范围内宣布研讨会，与会人数达到最高水平（第一天80人，随后两天40人）。与会者代表诺维奇大学，绿色山学院，和大鼠基因组数据库，以及11个部门/单位（4个学院）在UVM。 目标3：支持发展电子网络的行政基础设施（图2）。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，兴趣和进展，收集使用数据，将信息定向到参与者，并将顾问与保护者相匹配。这种支持是基于。这种基础设施已经在使用中;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发起了佛蒙特州科学和技术专家数据库的建设，该数据库的范围已经扩大到成为VGN ERIS项目。ERIS资源已被用于在全州范围内发布11项公告，并捕获25名UVM科学家的出版物和关键词索引。简要地说，ERIS的基本思想是利用公共人员目录、书目引用数据库、赠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通知、网页和自动通知参与者新条目的机器人进行交换。