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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 生物信息学核心的主要功能是提供最先进的序列分析和注释方面的专家咨询和分析，为 RI-INBRE 支持的研究人员制定复杂数据集分析的信息学策略，并对教职员工进行教育关于可能与其研究相关的生物信息学方法。 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，Daniel Udwary 博士兼职担任生物信息学核心协调员，Clinton Chichester 博士担任信息服务联合协调员。 全职生物信息学核心协调员 Joanna Fueyo 博士于 6 月加入 RI-INBRE 项目。 通过刺激基金提供的行政补助，为她提供了延长任期的机会。 她的资格包括博士学位。宾夕法尼亚大学医学院药理学博士学位，主修生物信息学。 她的专业知识包括多年在信息学系统和算法设计方面的私营行业经验，重点关注基因组、医学成像和临床数据集的集成和查询。 此外，她还拥有教授基本局部比对搜索工具 (BLAST) 算法及其在序列注释和治疗靶点发现方面的应用的研究生课程的经验。 她之前曾受雇于 IBM 医疗保健和生命科学公司，作为药物基因组学和医学领域的主题专家以及医学成像领域的团队负责人，在跨国咨询项目中服务了六年多。 在她之前在 SmithKline Beecham 和宾夕法尼亚大学工作期间，她成功地将算法及其衍生物应用于发现新型抗菌序列。 她还在她共同创立的 Infoceutics Inc. 公司中大规模应用 BLAST 来比较微生物序列数据中的基因组和蛋白质组。 生物信息学软件： 由于 Accelrys 已停止支持该软件，因此生物信息学核心中不再提供 GCG 软件包。 主要本科院校 (PUI) 和 URI 的核心提供的主要软件是 Sequencher。 URI 还提供一套分子建模软件（来自 Accelrys 的 Discovery Studio），我们在去年为此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该核心设施中可用软件的更详细列表。 核心目前也在评估其他生物信息学软件需求。使用许多算法、数据库和一些在线免费提供的软件进行数据分析。 例如，许多咨询请求严重依赖于全球精选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网络的，与这些序列相关的数据集（例如文献或精选文献资源）也是如此。 咨询请求中访问的大多数内容都是通过互联网进行的，因为数据在网络空间中以数字方式“链接”。因此，随着时间的推移，预计对商业软件包的依赖将会减少，并转向免费提供的、基于互联网的最先进的工具，这些工具与全球最新的序列和数据存储库相连。 生物信息学指导和咨询： 生物信息学核心为 RI-INBRE 支持的教师及其博士前和博士后研究人员提供有关推荐方法的指导和咨询。 自从加入 RI-INBRE 项目以来，Fueyo 博士拜访了 URI 和 PUI 的所有 RI-INBRE 研究人员，以了解有关他们研究的更多信息，并确定生物信息学方面潜在的咨询或合作领域。 这些访问产生了若干咨询请求，其中第一个请求已于去年夏天完成，其他请求最近收到并计划于 2010 年启动。当前的项目请求之一涉及确定最先进的网络-现有的工具用于按顺序分析转录因子结合位点，然后使用这些工具并对其他人进行使用这些工具的培训，包括制定正确使用这些工具的工作流程和策略。请求这项工作的研究人员希望咨询能够导致包括生物信息学分析在内的结果的发表。 RI-INBRE 支持的科学家在区域会议上进行的许多海报展示已经承认使用 RI-INBRE 生物信息学核心设施。 为了鼓励持续推广和提高对核心可以提供的咨询服务的认识，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清单。随着项目的完成和新方法的出现，这些材料将发布在 RI-INBRE 网站上。 生物信息学核心教学参与： 生物信息学核心人员提供生物信息学教学课程指导。 Udwary 博士是 2009 年春季跨学科研究生课程的联合讲师。在这门课程中，每个学生都需要与 URI 教员合作设计和实施一个创新的、原创的生物信息学研究项目。 学生们完成了 7 个高质量项目，其中许多项目现已应用于研究实验室，并可能会发表。 2009 年秋季，Fueyo 博士在研究生水平的技术课程中讲授了序列比对的理论基础，包括多重序列比对 (MSA)、BLAST 及其衍生物如何应用于序列数据的功能分配（注释）以及如何治疗可以使用 BLAST 在微生物基因组中识别目标。 她还教授基因组定向技能，使学生能够弄清楚他们在基因组中的位置，以及基因在基因组中的空间位置在生物学上意味着什么。 明年她或许还有机会继续参与正式的教学活动。 讲习班和研讨会的发展： 自 2010 年 1 月起，Fueyo 博士与 RI-INBRE 项目总监一起组织每月一次的 RI-INBRE 研讨会系列。 计划在下一财年的研讨会系列中更加关注生物信息学。 2009年秋，她邀请哈佛医学院的Martha Shenton博士做了题为“精神分裂症及相关疾病的磁共振（MR）和弥散张量成像（DTI）发现”的研讨会。 生物信息学核心将评估 RI-INBRE 教师的需求，并开发一个渐进的项目来满足这些需求。 其结果之一将是举办一系列生物信息学研讨会，以增进对计算方法能力的理解，从而增强他们的研究。 数据收集和管理以及网站管理： 目前的 RI-INBRE 记录正在被扫描和存储，以进行数字存档和检索。 未来，报告、调查和大多数其他数据将以电子方式收集，以便于数据仓储和搜索。 我们现在的网站是几年前由核心人员开发的。 目前由行政核心人员执行的网站更新和维护功能将恢复到生物信息学核心人员。 视频会议： 我们正在增加视频会议设备的使用。每个参与机构都提供了此类设备，从而增加了对 RI-INBRE 研讨会、指导委员会会议和东北网络基础设施网络 (NECC) 会议等活动的参与。 增强网络基础设施： NECC 成立于 2006 年，旨在评估网络基础设施需求并寻找改善宽带连接的方法，从而改善罗德岛州、缅因州、新罕布什尔州、佛蒙特州和特拉华州各研究机构之间的数据共享。 每个州的 NECC 项目分别由 NSF 和 NIH 通过 EPSCoR 和 INBRE 计划资助。 行政补充除了为延长全职生物信息学家的任命提供财政支持外，还规定在 URI 和该州北部现有宽带网络之间安装高速光纤。 目前，该项目正处于规划阶段。 Chichester 博士是 NECC 技术委员会的成员，该委员会将于 2010 年 3 月在佛蒙特州伯灵顿举行会议，协调全州范围内的各个项目。 会议出席和演讲： 生物信息学核心已经进行了许多演讲，其他演讲即将推出。 Fueyo 博士在 2009 年 8 月的夏季本科生研究员会议上展示了一张基于 RI-INBRE 咨询的海报。她还在 2009 年 8 月新罕布什尔州东北地区 IDeA 研讨会上做了受邀演讲，会上她谈到了“网络-促进 INBRE 及其他领域的研究合作”。 此外，她还参加了 2009 年秋季在布朗大学举行的仅限受邀者参加的高性能计算活动。她还受邀在布朗大学发表了一场关于“精神分裂症中的复杂脑网络分析”的演讲，这是她自己的研究兴趣领域。佛蒙特大学，2010 年 4 月。