"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.

摘要 计算生物学正日益成为生物科学研究中不可缺少的组成部分 技术进步提高了数据的能力和深度，调查人员可以接触到这些数据。 计算生物学和生物信息学资源对于本P01以RNA为中心的目标更加关键。 在之前的项目期间，Core B致力于提供有效和及时的计算生物学和 向P01调查人员提供生物信息学服务，从而出版了11份与核心B有关的出版物。除了核心之外 B为了提高能力和效率，它为项目具体需求提供了定制分析软件， 并为初级P01调查人员提供计算生物学和生物信息学培训。具体地说，核心B 减少了用于RNA-SEQ、ATAC-SEQ和CHIP-SEQ的标准分析管道的数据处理时间 开发自动综合分析软件，在杜兰大学和 佛罗里达大学高性能计算机(HPC)集群。这些管道大幅削减了主要数据- 翻译次数，其综合性为P01人员提供了很高的价值。自动化的 这些管道的性质还减少了核心B人员的操作时间，使他们能够投入更多精力 用于其他任务，如开发新的计算方法和教学。在之前的项目中 在此期间，核心B还开发了7个以上的软件包，直接响应项目1、2的需求 3.最后，核心B利用多管齐下的方法培训初级P01调查员，为他们配备 强大的计算机编程和数据分析技能，将帮助他们利用不断增长的 计算生物学和生物信息学在生物医学科学中的重要性。在下一个项目期间，核心B 将继续为P01调查人员提供快速全面的服务，提高工作效率和 核心B的能力，开发新的软件包以满足项目1、2和3的需求，并继续 培训计算生物学和生物信息学方面的下一代伽马疱疹病毒学家。