Bioinformatics Core

生物信息学核心

• 批准号: 8692921
• 负责人: Raphael D. Isokpehi
• 金额: $ 5.86万
• 依托单位: UNIVERSITY OF SOUTHERN MISSISSIPPI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8692921
• 关键词: Address; Advertising; Algorithms; Amino Acid Sequence; Applications Grants; Area; Awareness; Bioinformatics; Biological; Biomedical Research; Collaborations; Collection; Complex; Computer software; Consensus; Consultations; Continuing Education; Cystic Fibrosis Transmembrane Conductance Regulator; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Development; Dimensions; Educational Curriculum; Educational workshop; Exposure to; Extensible Markup Language; Faculty; Gene Expression; Gene Proteins; Generations; Generic Drugs; Genomics; Goals; Graph; Image; Informatics; Institution; Internet; Ions; Knowledge; Lead; Learning; Literature; Mass Spectrum Analysis; Mentors; Methodology; Methods; Microscope; Mississippi; Molecular; Ontology; Output; Paper; Pathway interactions; Peer Review; Peptide Sequence Determination; Phylogenetic Analysis; Population Analysis; Procedures; Progress Reports; Protein Structure Initiative; Proteins; Proteomics; PubMed; Reading; Research; Research Personnel; Research Project Grants; Resources; Secure; Sequence Analysis; Series; Services; Solutions; Structure; Students; System; Systems Biology; Testing; Text; Training; Training and Infrastructure; Travel; Universities; Visit; Visual; abstracting; base; bioimaging; cohort; computer program; computerized data processing; cyber infrastructure; data exchange; data mining; data sharing; design; experience; field study; genetic analysis; genome analysis; graduate student; improved; indexing; interdisciplinary collaboration; journal article; literacy; meetings; protein aminoacid sequence; protein metabolite; research study; science education; skills; text searching; tool; web site

Bioinformatics Core (Aim #1 and 2) The specific goals of the MS-INBRE Bioinformatics Core are: 1) build on existing interdisciplinary collaborations; 2) create new collaborative efforts between the PUIs and the research intensive universities; 3) train PUI students in bioinformatics; and 4) help address the serious cyberinfrastructure needs in Mississippi. To reach these goals the bioinformatics core will focus on improving bioinformatics awareness and literacy in Mississippi. The Bioinformatics Core will assist the PUI investigators with their scientific needs (Aim #1). Based on past experience (see "Progress Report" section for example), we envision that the following services will meet the scientific needs of PUI investigators: 1) Design and implementation of bioinformatics methods needed for projects. Bioinformatics solutions to research questions often require the integration of multiple bioinformatics methods in a computational pipeline. Increasingly, the use on spreadsheets by research investigators and students to manage and analyze results is also not optimal for comprehensive discovery of biological implications from data. The lack of expertise for these types of bioinformatics solutions could limit the research questions pursued and reduce the overall impact of the research project. Likely common small-scale bioinformatics analysis will include sequence and structure and phylogenetic analysis. Extracting information from literature databases is also a need for research projects that the Core can provide expertise. More complex analysis could include gene, protein and metabolite expression. As an example. Dr. Heda, a PUI investigator at MUW, utilized proteomics to study the cystic fibrosis transmembrane conductance regulator (CFTR). This project will generate large amounts of mass-spectrometry datasets in form of ion spectra that must be assigned to peptide sequences as well as inferences on protein abundances. The core will provide training for Dr. Heda and his students on understanding of the data exchange formats associated with mass spectrometry experiments such as mzML, TraML, mzldentML, mzQuantML and PSI-MI XML. 2) Advise on hardware and software needs for data storage, data sharing and data analysis. Types of data input or outputs associated with MS-INBRE projects include images from microscopes, tables of data, graphs, genomic and protein sequences, molecular pathway diagrams, videos of experiments and audio files. The data storage, sharing and analysis needs of MS-INBRE research projects vary depending on the data type. Thus the solution for each project will be customized. A critical need to facilitate research collaboration among MS-INBRE researchers is the implementation of a cyberinfrastructure for seamless and secure storage of data. In some cases, it is desired to have data storage, analysis and sharing to be accessible off-line and via a website. Visual analytics tools are making it possible for these data processes to be done together with minimal computer programming. 3) Contribute to grant proposals. The Bioinformatics Core will help provide preliminary data appropriate for inclusion in grant proposals. This data generation will be done in consultation with the collaborative research investigator. Standard or customized text for inclusion in the grant proposals will also be provided to investigators. The aim of this effort is to strengthen the research projects by adding the appropriate bioinformatics components. This is particulariy critical for PUI investigators. 4) Other technical services. The Core will provide assistance with the following bioinformatics topics: (1) Genome analysis; (2) Sequence analysis; (3) Phylogenetics; (4) Structural bioinformatics; (5) Gene expression; (6) Genetic and population analysis; (7) Systems biology; (8) Data and text mining; (9) Databases and ontologies and (10) Bioimage Informatics. Bioinformatics Literacy Project (Aim #2). Biomedical research involves the management and analysis of large and complex datasets requiring an understanding of a variety of bioinformatics software and databases. An urgent need identified by the MS-INBRE Bioinformatics Core is the need to build up the expertise of investigators and students at the PUIs in bioinformatics. The Bioinformatics Core has developed several tools that target PUIs. This is a critical need because PUIs do not have significant access or exposure to bioinformatics as an area of study. These tools will contribute to the development ofthe student pipeline into biomedical research. We have developed a Bioinformatics Literacy Project that will begin to address this issue. We believe that full implementation of this project at the PUIs will lead to the training of a large cohort of students in bioinformatics. The training components of this project are: 1) Bioinformatics Test Bank System. In this training infrastructure component, cohorts of trained graduate students at the core director's institution (JSU) read peer-reviewed bioinformatics articles and construct questions along with multiple-choice answers in the bioinformatics research areas. Questions are scored resulting in consensus questions. The Bioinformatics Test Bank system when fully developed will provide a resource for self-directed bioinformatics training, continuing education as well as competency testing. These questions will also be used in the bioinformatics traveling workshops at the PUIs. Ultimately however, the goal ofthe core is to infuse these modules into the science education curricula at the PUIs. 2) Bioinformatics Text Annotation. With a similar goal as above, experienced graduate students will help develop the bioinformatics curriculum by developing tools that facilitate learning. The abstract of a journal article on bioinformatics topics provides concise information about the article. The Sentence Annotation training infrastructure component was implemented to characterize sentences in abstracts by Focus - type of the information conveyed by the statement. Focus dimensions can be classified into three various types: Scientific (S) discussing findings and discovery; Generic (G) stating general knowledge, clarifying the structure ofthe paper, etc.; Methodology (M)¿describing a procedure or a method. A database of categorized sentences can be a learning resource for understanding bioinformatics facts. We have developed sentence segmentation algorithm, which splits titte and abstracts for sets of citations indexed in PubMed into sentences. Further, a web resource to retrieve the sentences is available based on keyword and PubMed Identifier (http://genomics.jsums.edu/sentence/bioinformj_pubmed/). 3) Short Bioinformatics Research Projects. Short-term (1-6 months) bioinformatics research projects can help students develop specialized bioinformatics skills. The bioinformatics core is coordinating efforts to develop short-term project ts that students (PUI and others) can engage in remotely from their institution with guidance from the core director. A collection of projects will be used for mentored senior year projects as well as objectives for graduate student theses or dissertation. Short-term projects are envisioned to have a mentoring component that may require an initial visit to JSU for training, however student-initiated projects will also be encouraged. We believe that this activity, once fully developed, will become an important resource for students at the PUIs or other institutions who lack faculty with bioinformatics expertise. 4) Bioinformatics Training Workshops. We have designed a training workshop series to provide research-driven level-defined introductory and advanced training workshops for students and faculty in Mississippi. The following workshops have been developed: a. Introductory Bioinformatics I (Introduction, Sequence Analysis, Databases and Ontologies) b. Introductory Bioinformatics II (Genome Analysis, Phylogenetics, and Structural Bioinformatics) c. Advanced Bioinformatics I (Gene Expression, Genetic and Population Analysis) d. Advanced Bioinformatics II (Systems Biology, Data and Text Mining) These traveling workshops will be conducted at the PUIs so that they reach students who otherwise would not be exposed to bioinformatics as a field of study. They will also be used as a tool to advertise the bioinformatics core services to investigators at the PUIs. We also plan to use these traveling workshops to cultivate interdisciplinary collaborations between the PUIs and research-intensive universities.

生物信息学核心（AIM＃1和2） MS-INBRE生物信息学核心的具体目标是：1）PUIS和研究密集型大学之间的新协作；生物信息学核心将着重于改善密西西比州的生物信息学意识和识字能力。 生物信息学核心核心协助PUI调查人员满足其科学需求（AIM＃1）。 根据过去的经验（例如，请参见“进度报告”部分）遗物： 1）项目所需的设计和实施方法。 研究问题的生物信息学经常在计算机中的多种生物信息学方法的整合，研究人员在管理和分析结果的电子表格上也是对数据缺乏生物信息类型的生物学含义的信息。限制了追求的研究，并减少了整体上的渗透率。利用蛋白质组学来研究Cystem跨膜电导调节剂（CFTR）。 以及针对HEDA博士和学生的核心Wille培训的推论，并以质谱实验（例如MZML，TRAML，MZLDENTML，MZQUANTML，MZQUANTML和PSI-MI XML）进行了质谱。 2）就数据存储，数据共享和数据的硬件和软件需求提供建议 分析。 显微镜，数据表，图，基因组和蛋白质序列，分子途径图， 经验和音频文件的视频。 研究项目因数据类型而有所不同。 自定义。 在某些情况下实施用于无缝和安全的数据的网络基础结构。 希望有数据存储 分析工具使这些数据过程可以与最小化一起完成 计算机编程。 3）有助于授予建议。 适用于赠款提案。 合作研究者。 还向调查人员提供了努力的目的 适当的生物信息学组成部分。 4）其他技术服务。 主题：（1）基因组分析；（2）序列分析； 基因（6）遗传和人口分析； （9）数据库和本体论以及（10）生物图像信息学。 生物信息学扫盲项目（AIM＃2）。 分析大型和复杂数据集数据集，需要和理解多种生物信息学 软件和数据库。 建立生物信息学核心的专家和学生已经开发了严重的人，这是一个至关重要的需求。意志为生物医学研究的开发做出了贡献。 在PUI中，将导致对大量学生进行生物信息学的培训。 该项目的组成部分是： 1）生物信息学测试银行系统。 核心导演学院（JSU）的培训研究生阅读了同行评审的生物信息学 文章和施工问题以及生物信息学研究中的多项选择答案 领域的评分导致共识问题。这些模块进入了PUI的科学教育课程。 2）生物信息学文本注释。 学生将有助于学习的生物信息学课程。等等；基于关键字和PubMed标识符，可以选择一个程序或方法。 （http://genomics.jsums.edu/sentence/bioinformj_pubmed/）。 3）短期生物信息学研究项目。 项目可以帮助学生发展专业的生物信息学技能。对于受过指导的高年级项目以及研究生论文或论文的目标。 短期项目被认为是JSIT对JSU进行培训的组件，我们也将鼓励我们认为这项活动将成为Atto PUI或其他缺乏的学生的重要资源具有生物信息学专业知识的教师。 4）生物信息学培训研讨会。 为密西西比州的学生和教职员工提供研究定义的入门和高级培训研讨会。 a简介生物信息学I（简介，序列分析，数据库和OND本体） b。 c。 d。 这些旅行研讨会将使学生成为研究，作为研究的工具工具也将成为生物信息学的工具。内置性。