INBRE: URI: BIOINFORMATICS CORE

INBRE：URI：生物信息学核心

• 批准号: 7960129
• 负责人: Daniel Wayne Udwary
• 金额: $ 7.49万
• 依托单位: UNIVERSITY OF RHODE ISLAND
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-04 至 2010-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7960129
• 关键词: Actinobacteria class; Actinomyces; Amino Acid Sequence; Anabolism; Anti-Inflammatory Agents; Anti-inflammatory; Area; Behavioral Research; Bioinformatics; Biological Factors; Biological Sciences; Biology; Biomedical Research; Chemical Structure; Chemistry; Collaborations; Communities; Computer Retrieval of Information on Scientific Projects Database; Computer software; Core Facility; DNA; DNA Sequence; Data; Discipline; District of Columbia; Education; Educational process of instructing; Educational workshop; Electronic library; Electronics; Faculty; Funding; Future; GCG gene; Gene Cluster; Genetic; Genome; Genomics; Goals; Grant; Hand; Indiana; Informatics; Institutes; Institution; Interdisciplinary Study; Joints; Journals; Laboratories; Learning; Licensing; Location; Marines; Metabolic; Molecular Models; National Center for Research Resources; New England; Nucleotides; Operative Surgical Procedures; Participant; Protein Tyrosine Phosphatase; Proteomics; Publications; Research; Research Personnel; Research Project Grants; Resources; Rhode Island; Running; Series; Services; Source; Specialist; Students; System; Tertiary Protein Structure; Training; United States National Institutes of Health; Universities; Update; Vermont; Work; Yin; base; chemical genetics; college; cyber infrastructure; experience; firewall; interest; lectures; marine natural product; medical schools; meetings; member; molecular modeling; outreach; posters; programs; protein structure; symposium; tool; user-friendly

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 goal of the Bioinformatics Core is to facilitate the analysis and interpretation of various types of data for RI-INBRE-supported investigators at the network institutions. The data types include nucleotide and amino acid sequences, protein domains, and protein structures. Then, by applying informatics, the Bioinformatics Core assists the researchers in understanding and organizing different types of information. A wide variety of software and hardware applications have been acquired by the Bioinformatics Core to assist in the analysis and interpretation of the data. In the future, the core will continue to develop bioinformatics courses, training sessions, lectures, and seminars. Dr. Daniel Udwary, a recently hired specialist in bioinformatics, coordinates the direction and activities of the Core. In the coming year, Dr. Udwary's focus will be to expand the core's outreach and instructional activities in order to increase the usage of the Bioinformatics Core services and software. Additionally, the Bioinformatics Core is currently working with the Northeast Cyberinfrastructure Consortium on an NIH proposal that will greatly enhance the cyberinfrastructure available to researchers throughout the Northeast. Bioinformatics Software: The major bioinformatics software continues to be our molecular modeling software, our GCG bioinformatics software, SeqLab and SeqWeb, and Sequencher. Last year UNIX based Insite II molecular modeling programs were converted to Accelrys's PC based Discovery Studio. A new Dell workstation was purchased so that these programs would run efficiently. Sequencher, a powerful user-friendly DNA sequence assembly and analysis software that results in high quality, reliable DNA contigs was added two years ago. A dedicated server for the Sequencher license enabled users to log on from various locations. We increased the number of licenses so that all users at the Primarily Undergraduate Institutions (PUIs) that needed Sequencher had access. A stand alone version of the application is deployed at the PUIs where needed. Video Conferencing: A video conferencing network was implemented over the last 18 months. Each of the network institutions received a mobile cart with full video and data conferencing capabilities based on the Polycom VSX7400. Each system contained dual 20" LCD screens and a mobile camera. All six of the mobile carts are deployed, one at each network institution. Last year, firewall and network issues added to the complexity of the deployment, but these have been resolved. Conferences have been conducted throughout the network and between other INBREs in the Northeast. The core has also initiated broadcasts of the RI-INBRE seminar series allowing for increased participation by the Network institutions. Bioinformatics Classes and Training Session(s): The recent hiring of Dr. Udwary at the University of Rhode Island (URI) expands our offering in bioinformatics. For the eighth consecutive year, a graduate level bioinformatics class was offered at the University of Rhode Island. This year the class was taught by Dr. Udwary, who has initiated research projects that resulted in collaborations among faculty from varied disciplines in informatics and the biological sciences. Student projects were especially successful, with many continuing as directed studies and MS thesis topics. Together with Dr. Bethany Jenkins in CELS, Dr. Udwary will develop a new course in undergraduate bioinformatics that is less research oriented and more "hands-on", this will allow undergraduate students to learn access and most importantly utilize bioinformatics tools. We continue to have workshop sessions. Dr. James Vincent from The Vermont Genetics Institute came to URI and led a discussion as to the types of bioinformatics resources that are available at the VT-INBRE. This was the first of a series of sessions where other bioinformatics core leaders in the area will be brought in and the scope of their operations discussed. In addition, discussions were held with the RI-EPSCOR office concerning bioinformatics. We investigated possible areas of overlap and ways that the RI-INBRE and RI-EPSCOR could collaborate. It was decided that both groups would hold joint bioinformatics seminars which will allow for larger audiences and a greater number of presentations. Outreach Efforts: We continue to develop a formal relationship with the Community College of Rhode Island (CCRI) to provide CCRI faculty with training and access to bioinformatics software. Faculty members at CCRI have begun utilizing available bioinformatics tools and integrating such material into existing courses. This relationship has allowed CCRI faculty to introduce their students to bioinformatics and will continue to enhance the laboratory experience for CCRI students. The RI-INBRE investigators at the primarily undergraduate institutions were granted access to the electronic library resources at the University of Rhode Island last year. This has greatly increased their access to electronic journals. Additional outreach efforts include bioinformatics seminars which are open to all interested parties. One such seminar included a presentation by Dr. Zhong-Yin Zhang from the Indiana University School of Medicine entitled "Chemical Genetic and Proteomic Studies of Protein Tyrosine Phosphatases". Presentations: In November a poster was presented by the Bioinformatics Core at the 3rd Annual Biology New England South (BioNES) meeting at Roger Williams University on December 2, 2008. In addition, a poster focusing on RI-INBRE bioinformatics tools and resources was presented at the RI-INBRE Research Fellows Meeting and Faculty Retreat at Roger Williams University in Bristol, RI on January 30, 2009. At that meeting, RI-INBRE-supported investigators were polled as to their bioinformatics needs and usage. The RI-INBRE Bioinformatics Core was also a participant and presenter at the Cyber infrastructure Workshop held at the NIH, NCRR 2nd Biennial IDeA Symposium of Biomedical Research Excellence (NISBRE) in Washington, DC on August 6-8, 2008. Dr. Udwary also promoted the bioinformatics core by presenting various seminars including "Secondary metabolic gene clusters from the genome of the marine actinomycete, Salinispora arenicola CNS-205" and "Biosynthesis of cyclomarin, an anti-inflammatory cyclic heptapeptide produced by Salinispora arenicola" at the Gordon Conference on Marine Natural Products in Ventura, CA on February 24-29, 2008, "Accessing genomic data for the prediction and elucidation of actinomycete natural product chemical structures" at the Department of Chemistry, Brown University on April 8, 2008, and "Chemical genetics: Examples from the marine actinomycete genus, Salinispora" during the Interdisciplinary Research Seminar Series at the University of Rhode Island on March 7, 2008. Summary: Throughout 2008, education and updating of bioinformatics software has significantly increased the volume and depth of usage of all aspects of our bioinformatics core. As a result of the increased usage, eight publications in the last year have acknowledged use of the RI-INBRE Bioinformatics Core Facility. In addition the RI-INBRE Bioinformatics Core was a participant in the Northeast Network Initiative (NENI) to advance cyber infrastructure throughout the northeast. The core was also a participant in the EPSCoR Track II proposal that will further expand cyberinfrastructure in the Northeast if funded. A similar INBRE proposal for enhancing cyberinfrastructure in the Northeast, including RI, will be submitted on March 1, 2009.

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表示。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目的是促进网络机构中RI INBRE支持的研究人员的各种类型数据的分析和解释。 数据类型包括核苷酸和氨基酸序列，蛋白质结构域和蛋白质结构。 然后，通过应用信息学，生物信息学核心有助于研究人员理解和组织不同类型的信息。生物信息学核心已经收集了各种软件和硬件应用程序，以帮助对数据的分析和解释。 将来，核心将继续开发生物信息学课程，培训课程，讲座和研讨会。 最近聘用的生物信息学专家Daniel Udwary博士协调了核心的方向和活动。在来年，Udwary博士的重点将是扩大核心的外展和教学活动，以增加生物信息学核心服务和软件的使用。此外，生物信息学核心目前正在与东北网络基础设施联盟合作，在NIH提案中，将大大增强东北研究人员可用的网络基础设施。 生物信息学软件：主要的生物信息学软件继续是我们的分子建模软件，我们的GCG生物信息学软件，Seqlab和Seqweb以及Sequencher。 去年，基于Unix的INSITE II分子建模程序被转换为Accelrys基于PC的Discovery Studio。 购买了一个新的戴尔工作站，以便这些程序有效地运行。 Sequencher是一种强大的用户友好的DNA序列组装和分析软件，两年前添加了高质量，可靠的DNA重叠群。 Sequencher许可证的专用服务器使用户可以从各个位置登录。 我们增加了许可证的数量，以便所有需要续签器访问的本科机构（PUI）的所有用户都可以访问。 该应用程序的独立版本在需要的地方部署在PUI上。 视频会议：在过去的18个月中实施了视频会议网络。每个网络机构都收到了一个基于Polycom VSX7400的完整视频和数据会议功能的移动购物车。每个系统都包含双20英寸LCD屏幕和一个移动摄像头。部署了所有六个移动车，一个在每个网络机构中。去年，防火墙和网络问题增加了部署的复杂性，但已解决。会议。会议。会议。在整个网络中以及东北部的其他内心之间进行了进行。 生物信息学课程和培训课程：罗德岛大学（URI）最近聘用Udwary博士的招聘，扩大了我们在生物信息学领域的产品。 连续第八年，罗德岛大学提供了一级生物信息学课程。今年，该课程是由Udwary博士教授的，Udwary博士启动了研究项目，从而导致了来自多样化的信息学和生物科学学科的教师之间的合作。学生项目尤其成功，许多人按照指导性研究和论文主题继续进行。 Udwary博士与Cels的Bethany Jenkins博士一起，将开发一门新课程的本科生物信息学课程，该课程较少，研究较少，更“动手”，这将使本科生能够学习访问权限，并最重要的是使用生物信息学工具。 我们继续举办研讨会。 佛蒙特州遗传学研究所的詹姆斯·文森特（James Vincent）博士来到URI，并讨论了VT-Inbre上可用的生物信息学资源的类型。 这是一系列会议中的第一次，该会议将引入该地区的其他生物信息学核心领导者，并讨论了其运营的范围。 此外，与RI-EPSCOR办公室有关生物信息学的讨论进行了讨论。 我们调查了RI-INBRE和RI-EPSCOR可以合作的可能重叠领域。 决定两组将举办联合生物信息学研讨会，这将允许更多的受众和更多的演讲。 推广工作：我们继续与罗德岛社区学院（CCRI）建立正式的关系，以向CCRI教师提供培训和使用生物信息学软件。 CCRI的教职员工已经开始利用可用的生物信息学工具，并将这些材料集成到现有课程中。 这种关系使CCRI教师能够向学生介绍生物信息学，并将继续增强CCRI学生的实验室体验。 去年，主要是本科机构的RI-INBRE调查员被授予了罗德岛大学的电子图书馆资源。 这大大增加了他们获得电子期刊的访问。 额外的推广工作包括向所有有关方面开放的生物信息学研讨会。 一个这样的研讨会包括印第安纳大学医学院的钟杨博士的演讲，标题为“蛋白质酪氨酸磷酸酶的化学遗传和蛋白质组学研究”。 演讲：11月2日在罗杰·威廉姆斯大学（Roger Williams University）举行的第三届年度生物学新英格兰南部（Biones）会议上，生物信息学核心向2008年12月2日举行了一张海报在2009年1月30日在RI的RI-INBRE研究研究员会议和教职员工撤退。 RI-Inbre BioInformatics Core还是在NIH举行的网络基础设施研讨会的参与者和演示者。通过提出各种研讨会，包括“来自海洋放线菌基因组的次生代谢基因簇，萨利尼斯波拉竞技场CNS-205”和“环胞果生物合成的生物合成，一种抗感染的环肽的抗激症状乳肽，由salinispora eranicpora artinicpora Attate at At ant At ant Atat At ant Attate and，促进了生物信息学的核心。 2008年2月24日至29日，加利福尼亚州文图拉的海洋天然产品“访问基因组数据，以预测和阐明放线菌天然产物化学结构的预测和阐明”，布朗大学化学系于2008年4月8日，化学基因因： 2008年3月7日，在罗德岛大学的跨学科研究研讨会系列中，来自萨利尼普拉族海洋放线菌属的例子。 摘要：在整个2008年，生物信息学软件的教育和更新大大增加了生物信息学核心各个方面的使用量和深度。 由于使用的增加，去年的八本出版物承认使用了RI-INBRE生物信息学核心设施。 此外，RI-INBRE生物信息学核心是东北网络计划（NENI）的参与者，旨在推进整个东北地区的网络基础设施。 核心也是EPSCOR TRACK II提案的参与者，如果资助，将进一步扩大东北的网络基础设施。 将于2009年3月1日提交类似的增强包括RI的网络基础设施的近亲提案。