INBRE: URI: BIOINFORMATICS CORE

INBRE：URI：生物信息学核心

• 批准号: 8167601
• 负责人: JOANNA L FUEYO
• 金额: $ 5.51万
• 依托单位: UNIVERSITY OF RHODE ISLAND
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8167601
• 关键词: Administrative Supplement; Algorithms; Appointment; Area; Arts; Award; Awareness; Back; Base Sequence; Binding Sites; Bioinformatics; Biological Sciences; Brain; Clinical Data; Collaborations; Complex; Computer Retrieval of Information on Scientific Projects Database; Computer software; Computing Methodologies; Consult; Consultations; Core Facility; Data; Data Analyses; Data Collection; Data Set; Databases; Delaware; Dependence; Development; Diffusion Magnetic Resonance Imaging; Disease; Docking; Doctor of Philosophy; Educational process of instructing; Educational workshop; Employment; Equipment; Event; Faculty; Fiber; Financial Support; Funding; Future; GCG gene; Genes; Genome; Genomics; Grant; Healthcare; High Performance Computing; Human Resources; Industry; Informatics; Information Services; Institution; Instruction; Internet; Laboratory Research; Lead; Learning; Link; Literature; Magnetic Resonance; Maine; Maintenance; Maps; Medical Imaging; Medicine; Molecular Models; New Hampshire; Online Systems; Pathway Analysis; Pennsylvania; Pharmacogenomics; Pharmacology; Postdoctoral Fellow; Proteins; Proteome; Publications; Records; Reporting; Research; Research Personnel; Research Project Grants; Resources; Retrieval; Rhode Island; Scanning; Schizophrenia; Scientist; Sequence Alignment; Sequence Analysis; Series; Services; Source; Speed; Staging; Stimulus; Students; Surveys; System; Techniques; Time; Training; United States National Institutes of Health; Universities; Update; Vermont; Visit; Work; antimicrobial; base; data sharing; design; digital; experience; falls; improved; innovation; instructor; interest; lectures; medical schools; meetings; member; methionylmethionine; microbial; microbial genome; molecular modeling; novel; novel strategies; outreach; posters; programs; repository; skills; symposium; therapeutic target; tool; transcription factor; web site

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. The primary functions of the Bioinformatics Core are to provide expert consultation and analysis in state-of-the-art sequence analysis and annotation, to develop informatics strategy for analysis of complex data sets for RI-INBRE-supported investigators, and to educate the faculty regarding Bioinformatics approaches which may be relevant to their research. The responsibilities of the Core also include other activities such as website management, data collection and storage for the RI-INBRE Program, and coordination of the monthly RI-INBRE seminar series. Until May 2009, Dr. Daniel Udwary served as the Bioinformatics Core Coordinator on a part-time basis, with Dr. Clinton Chichester as the Co-Coordinator for information services. A full-time Bioinformatics Core Coordinator, Dr. Joanna Fueyo, joined the RI-INBRE Program in June. An opportunity to extend her appointment was provided through an administrative supplement awarded from stimulus funds. Her qualifications include a Ph.D. in Pharmacology from the University of Pennsylvania School of Medicine with a concentration in Bioinformatics. Her expertise includes several years of private industry experience in informatics system and algorithm design, with a focus on the integration and query of genomic, medical imaging, and clinical data sets. In addition, she has experience teaching graduate courses on the Basic Local Alignment Search Tool (BLAST) algorithm and its application to both sequence annotation and therapeutic target discovery. She was formerly employed by IBM Healthcare and Life Sciences where she served on multi-national consulting projects for over six years as a subject matter expert in Pharmacogenomics and Medicine and as team leader in Medical Imaging. During two of her former employments at SmithKline Beecham and the University of Pennsylvania, she successfully applied the algorithm and its derivatives to the discovery of novel anti-microbial sequences. She also has applied BLAST on a large scale for genome and proteome comparison in microbial sequence data in the company she co-founded, Infoceutics Inc. Bioinformatics Software: The GCG package is no longer offered in the Bioinformatics Core since Accelrys has stopped supporting this software. The main software provided by the Core at the primarily undergraduate institutions (PUIs) and at URI is Sequencher. Also available at URI is a suite of molecular modeling software (Discovery Studio from Accelrys), for which we purchased a new protein-protein docking module during the past year. A more detailed list of the software available in this Core Facility is described in the bioinformatics section of Shared Facilities. The Core is currently evaluating other Bioinformatics software needs as well. A number of algorithms, databases, and some software that is freely available online were utilized for data analysis. For instance, many of the consultation requests rely heavily on sequence data located in world-wide curated databases. The algorithms that analyze these sequence repositories are typically web-based, as are the datasets that are relevant to these sequences, such as literature or curated literature resources. Most everything accessed in a consultation request is via the internet since the data is numerically 'linked' in cyberspace. Therefore, over time it is anticipated that there will be a decreased dependence on commercially available software packages and a move towards freely available, internet-based state-of-the-art tools that are linked to the most recent sequence and data repositories worldwide. Bioinformatics Instruction and Consultation: The Bioinformatics Core provides instruction and consultation for the RI-INBRE-supported faculty and their pre- and post-doctoral researchers on the recommended approach. Since joining the RI-INBRE Program, Dr. Fueyo has visited all of the RI-INBRE investigators at URI and at the PUIs to learn more about their research and in order to identify potential areas for consultation or collaboration in Bioinformatics. These visits have resulted in several consultation requests, the first of which was completed last summer, and others which were recently received and are planned for initiation in 2010. One of the current project requests involves determining what state-of-the-art web-based tools exist for the analysis of transcription factor binding sites in sequence, followed by use of these tools and training of others in the use of these tools, including mapping out a workflow and strategy for their correct utilization. The investigators requesting this work hope that the consultation can lead to publication of the results including the Bioinformatics analysis. A number of poster presentations by RI-INBRE-supported scientists at regional conferences have already acknowledged use of the RI-INBRE Bioinformatics Core Facility. To encourage continued outreach and awareness of the consultation services the Core can provide, the Bioinformatics Core is creating a list of key bioinformatics consultative skills and strategic approaches that are relevant to RI-INBRE investigators. These materials will be put on the RI-INBRE website as projects are completed and as new approaches become available. Bioinformatics Core Involvement in Teaching: The Bioinformatics Core personnel provided didactic course instruction in Bioinformatics. Dr. Udwary was a co-instructor in a cross-disciplinary graduate-level course in spring 2009. In this class, each student was required to design and implement an innovative, original Bioinformatics research project in collaboration with a URI faculty member. Students completed 7 high-quality projects, many of which are now being applied in the research laboratories and may lead to publications. In fall 2009 Dr. Fueyo lectured in a graduate-level techniques course and taught the theoretical basis of sequence alignment including multiple sequence alignment (MSA), how BLAST and its derivatives are applied to functional assignment of sequence data (annotation), and how therapeutic targets can be identified in microbial genomes, using BLAST. She also taught Genome Orientation skills that enabled the students to figure out where they are within a genome, and what the spatial placement of a gene in a genome means biologically. She may have the opportunity to continue her participation in the formal teaching activities next year. Workshop and Seminar Development: As of January 2010, Dr. Fueyo, in conjunction with the RI-INBRE Program Director, is now organizing the monthly RI-INBRE seminar series. An increased focus on Bioinformatics in the seminar series during the next fiscal year is planned. In fall 2009, she invited Dr. Martha Shenton of Harvard Medical School to give a seminar entitled, "Magnetic Resonance (MR) and Diffusion Tensor Imaging (DTI) Findings in Schizophrenia and Related Disorders". The Bioinformatics Core will be evaluating the needs of the RI-INBRE faculty and developing a progressive program to meet those needs. One result of this will be a series of workshops in Bioinformatics to increase the understanding of the capabilities of computational methods to enhance their research. Data Collection and Management, and Website Management: The present RI-INBRE records are being scanned and stored for digital archival and retrieval. In the future, reports, surveys, and most other data will be collected electronically in order to facilitate data warehousing and searches. Our present web site was developed a few years ago by the Core personnel. Updating and maintenance functions of the website that are currently performed by the Administrative Core personnel will revert back to the Bioinformatics Core. Video Conferencing: We are increasing the use of video conferencing equipment. The provision of this equipment at each of the participating institutions has led to increased participation in such activities as RI-INBRE seminars, Steering Committee meetings, and meetings of the Northeast Cyberinfrastructure Network (NECC). Enhancement of Cyberinfrastructure: NECC was formed in 2006 to assess the cyberinfrastructure needs and find ways to improve broad bandwidth connectivity, and thereby data sharing, between the various research institutions in Rhode Island, Maine, New Hampshire, Vermont and Delaware. The NECC projects were funded in each state by both NSF and NIH through EPSCoR and INBRE programs, respectively. The administrative supplement, besides providing financial support for extending the appointment of the full-time Bioinformatist, also provides for high speed fiber installation between URI and the existing broadband network in the northern part of the state. At present, this project is in its planning stage. Dr. Chichester serves on the NECC technical committee which will meet in Burlington ,VT in March, 2010 to coordinate the various statewide projects. Meeting Attendance and Presentations: The Bioinformatics Core has had a number of presentations and others are forthcoming. Dr. Fueyo presented a poster based on an RI-INBRE consultation at the Summer Undergraduate Research Fellows Conference in August 2009. She also gave an invited talk at the Northeast Regional IDeA Symposium in New Hampshire in August 2009, where she spoke about "Cyber-Enabled Research Collaborations in INBRE and Beyond". In addition, she attended an invite-only High Performance Computing event at Brown University, in Fall 2009. She has also been invited to present a talk on "Complex Brain Network Analysis in Schizophrenia", an area of her own research interest, at the University of Vermont in April 2010.

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。 生物信息学核心的主要功能是在最先进的序列分析和注释中提供专家咨询和分析，以制定信息学策略，以分析RI-INBRE支持的研究人员的复杂数据集，并教育有关与其研究可能与研究有关的生物信息学方法的教师。 核心的职责还包括其他活动，例如RI-INBRE计划的网站管理，数据收集和存储以及每月RI-INBRE研讨会系列的协调。 直到2009年5月，丹尼尔·乌德瓦里（Daniel Udwary）博士兼职担任生物信息学核心协调员，克林顿·奇切斯特（Clinton Chichester）博士是信息服务的协调员。 全职生物信息学核心协调员Joanna Fueyo博士于6月加入了RI-INBRE计划。 通过刺激基金授予的行政补品提供了扩展任命的机会。 她的资格包括博士学位。宾夕法尼亚大学医学院的药理学专业学院专注于生物信息学。 她的专业知识包括数年的信息系统和算法设计方面的私营企业经验，重点是基因组，医学成像和临床数据集的集成和查询。 此外，她还具有教学研究生课程，以基本的本地对齐搜索工具（BLAST）算法及其在序列注释和治疗目标发现中的应用。 她以前曾在IBM Healthcare和Life Sciences雇用，在跨国咨询项目中担任药物基因组学和医学领域的主题专家，并担任医学成像的团队负责人。 在她在Smithkline Beecham和宾夕法尼亚大学的两项以前的工作期间，她成功地将算法及其衍生物应用于新颖的抗微生物序列。 她还大规模应用爆炸，以在她共同创建的Infoceutics Inc.公司中的微生物序列数据中进行基因组和蛋白质组比较。 生物信息学软件： GCG软件包不再在生物信息学核心中提供，因为Accelrys已停止支持该软件。 核心在本科机构（PUI）和URI上提供的主要软件是续集者。在URI上也可以使用分子建模软件（Accelrys的发现工作室），为此我们在过去一年中购买了一个新的蛋白质 - 蛋白质对接模块。共享设施的生物信息学部分描述了此核心设施中可用的软件的更详细列表。 核心目前也正在评估其他生物信息学软件的需求。在网上免费获得的许多算法，数据库和某些软件都用于数据分析。 例如，许多咨询请求在很大程度上依赖于位于全球策划数据库中的序列数据。分析这些序列存储库的算法通常是基于Web的，与这些序列相关的数据集也是如此，例如文献或策展文献资源。 咨询请求中访问的大多数所有内容都是通过Internet进行的，因为数据在网络空间中“链接”。因此，随着时间的流逝，预计将依赖于市售软件包的依赖性以及朝着与全球最新序列和数据存储库相关联的自由获得的，基于Internet的最新工具的转变。 生物信息学指导和咨询： 生物信息学核心为RI-INBRE支持的教师及其前后研究人员提供了指导和咨询。 自加入RI-INBRE计划以来，Fueyo博士访问了URI和PUI的所有RI-INBRE调查人员，以了解有关他们的研究的更多信息，并为了确定生物信息学咨询或协作的潜在领域。 这些访问导致了几项咨询请求，其中的第一个访问是在去年夏天完成的，而其他访问请求是在2010年收到的，并计划在2010年进行启动。当前的一个请求之一涉及确定基于最新的Web的工具，以分析转录因子结合站点的依次分析，并在这些工具中使用这些工具和其他工具的培训，包括这些工具的使用，包括这些工具，包括努力和策略的策略和策略。要求这项工作的调查人员希望咨询能够导致结果发布，包括生物信息学分析。 RI-INBRE支持的科学家在地区会议上的许多海报演讲已经承认使用了RI-INBRE生物信息学核心设施。 为了鼓励核心可以提供的持续推广和对咨询服务的认识，生物信息学核心正在创建与RI-INBRE研究人员相关的关键生物信息学咨询技能和战略方法的清单。这些材料将在项目完成后将其放置在RI-Inbre网站上，并且随着新方法的可用性。 生物信息学核心参与教学： 生物信息学核心人员提供了生物信息学的教学教学。 Udwary博士是2009年春季跨学科研究生级课程的共同教师。在此课程中，每个学生都必须与URI教职员工合作设计和实施创新的，原始的生物信息学研究项目。 学生完成了7个高质量项目，其中许多项目现在正在研究实验室中应用，并可能导致出版物。 2009年秋季，Fueyo博士在研究生级技术课程中讲授，并教授了序列比对的理论基础，包括多个序列比对（MSA），如何将BLAST及其衍生物应用于序列数据的功能分配（注释）以及如何在Microbobial Genomes中使用爆炸质量确定治疗靶标。 她还教授了基因组取向技巧，使学生能够弄清楚基因组中的位置，以及基因组中基因的空间位置在生物学上意味着什么。 她可能有机会继续参加明年的正式教学活动。 研讨会和研讨会发展： 截至2010年1月，Fueyo博士与RI-INBRE计划总监一起，现在正在组织每月的RI-INBRE研讨会系列。 计划在下一个财政年度中，在研讨会系列中对生物信息学的关注越来越多。 2009年秋季，她邀请了哈佛医学院的玛莎·申顿（Martha Shenton）博士举行了一个题为“磁共振（MR）和相关疾病中的磁共振（MR）和扩散张量成像（DTI）的发现”。 生物信息学核心将评估RI-INBRE教师的需求，并制定一项进步计划以满足这些需求。 结果之一将是一系列生物信息学研讨会，以增加对计算方法增强其研究能力的理解。 数据收集和管理以及网站管理： 目前的RI-INBRE记录正在扫描并存储用于数字档案和检索。 将来，将以电子方式收集报告，调查和大多数其他数据，以促进数据仓库和搜索。 我们目前的网站是几年前由核心人员开发的。 管理核心人员当前执行的网站的更新和维护功能将恢复为生物信息学核心。 视频会议： 我们正在增加视频会议设备的使用。在每个参与机构的设备中提供此设备，导致参与RI-INBRE研讨会，指导委员会会议和东北网络网络基础设施网络（NECC）等活动。 网络基础设施的增强： NECC成立于2006年，旨在评估网络基础设施需求，并找到改善广泛带宽连通性的方法，从而在罗德岛，缅因州，新罕布什尔州，佛蒙特州和特拉华州的各个研究机构之间进行数据共享。 NECC项目分别由NSF和NIH通过EPSCOR和INBRE计划在每个州提供资金。 行政补充剂除了提供财政支持以扩展全日制生物信息主义者的任命外，还提供了URI和该州北部现有的宽带网络之间的高速光纤安装。 目前，该项目处于计划阶段。 Chichester博士在NECC技术委员会任职，该委员会将于2010年3月在VT伯灵顿开会，以协调各个全州项目。 会议和演讲： 生物信息学核心有许多演讲，而其他核心正在即将进行。 Fueyo博士在2009年8月在夏季的本科研究研究员会议上介绍了一份有关RI-INBRE咨询的海报。她还在2009年8月在新罕布什尔州的东北地区思想研讨会上发表了一场邀请的演讲，她在那里谈到了“网络支持的网络支持的研究协作Inbre and Beyond”。 此外，她于2009年秋季参加了布朗大学（Brown University）举行的仅邀请的高性能计算活动。她还被邀请在2010年4月在佛蒙特大学（University of Vermont）介绍“精神分裂症中复杂的脑网络分析”的演讲。