"Core B" Viral RNA-seq and bioinformatics Core

“核心 B”病毒 RNA-seq 和生物信息学核心

• 批准号: 10403019
• 负责人: ERIK K FLEMINGTON
• 金额: $ 21.52万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-02-09 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10403019
• 关键词: AIDS related cancer; ATAC-seq; Acquired Immunodeficiency Syndrome; Bioinformatics; Biological Sciences; Biology; Biomedical Research; Biomedical Technology; ChIP-seq; Clinical; Communities; Complex; Computational Biology; Computational Science; Computer software; Computing Methodologies; Custom; Data; Data Analyses; Development; Educational process of instructing; Ensure; Florida; Foundations; Goals; HIV; Health; Human; Human Herpesvirus 4; Human Herpesvirus 8; Human Resources; Individual; Infrastructure; Investigation; Kaposi Sarcoma; Lymphoma; Malignant Neoplasms; Modeling; Murine herpesvirus 68; Mus; Nature; Oncogenic; Persons; Positioning Attribute; Progress Reports; Publications; RNA; Research; Research Personnel; Research Project Grants; Research Training; Resources; Science; Sequence Analysis; Services; Site; Software Tools; Solid; Technology; Time; Training; Universities; Untranslated RNA; Viral; Work; analysis pipeline; arm; automated analysis; bioinformatics resource; career; comparative; computer cluster; computer program; computerized data processing; data standards; experience; gammaherpesvirus; high end computer; improved; inter-institutional; mouse model; next generation; next generation sequencing; operation; response; skills; tissue culture; tool; transcriptome sequencing; viral RNA

Summary Computational biology is becoming increasingly integral to biological science research as relentless technological advances increase the capabilities and depth of data that is put at arm’s reach of investigators. Computational biology and bioinformatics resources are even more critical for the RNA-centric goals of this P01. In the previous project period, Core B worked to provide effective and timely computational biology and bioinformatics services to P01 investigators, resulting in 11 Core B-associated publications. In addition to Core B working to improve capabilities and efficiency, it provided custom analysis software for project-specific needs, and provided computational biology and bioinformatics training to junior P01 investigators. Specifically, Core B reduced data processing times of standard analysis pipelines for RNA-seq, ATAC-seq, and ChIP-seq through the development of automated comprehensive analysis software that operates on the Tulane University and University of Florida High Performance Computer (HPC) clusters. These pipelines substantially cut primary data- to-interpretation times, and their comprehensive nature provides high value to P01 personnel. The automated nature of these pipelines also reduces Core B personnel operation time, allowing them to dedicate more effort to other tasks, such as development of new computational methods and teaching. During the previous project period, Core B also developed more than 7 software packages in direct response to the needs of Projects 1, 2 and 3. Lastly, Core B utilized a multipronged approach to train junior P01 investigators, arming them with powerful computer programming and data analysis skills that will help them take advantage of the growing importance of computational biology and bioinformatics in biomedical science. In the next project period, Core B will continue to provide rapid and comprehensive services to P01 investigators, increase the efficiency and capabilities of Core B, develop new software packages to meet the needs of Projects 1, 2, and 3, and continue to train the next generation of gammaherpesvirologists in computational biology and bioinformatics.

概括 计算生物学越来越成为生物科学研究的不可或缺 技术进步增加了研究人员触及的数据的功能和深度。 计算生物学和生物信息学资源对于以RNA为中心的目标至关重要。 在上一个项目时期，核心B致力于提供有效，及时的计算生物学，并 P01调查人员的生物信息学服务，导致11个核心相关出版物。除了核心 b致力于提高能力和效率，它为项目特定需求提供了自定义分析软件， 并为初级P01研究者提供了计算生物学和生物信息学培训。具体而言，核心b 通过RNA-SEQ，ATAC-SEQ和CHIP-SEQ的标准分析管道的数据处理时间减少 在杜兰大学和 佛罗里达大学高性能计算机（HPC）集群。这些管道大大削减了主要数据 - 到解释时间及其全面的性质为P01人员提供了高价值。自动化 这些管道的性质也减少了核心B人事工作时间，使他们能够付出更多的努力 到其他任务，例如开发新的计算方法和教学。在上一个项目中 时期，Core B还开发了7个以上的软件包，直接响应项目1、2的需求 和3。最后，核心B使用多管齐下的方法来培训初级P01调查员，并用 强大的计算机编程和数据分析技能，将有助于他们利用增长 在生物医学科学中计算生物学和生物信息学的重要性。在下一个项目期间，核心B 将继续为P01调查人员提供快速而全面的服务，提高效率和 核心B的功能，开发新的软件包以满足项目1、2和3的需求，然后继续 培训计算生物学和生物信息学领域的下一代伽马犬科学家。