"Core B" Viral RNA-seq and bioinformatics Core

“核心 B”病毒 RNA-seq 和生物信息学核心

基本信息

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
项目类别：
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

项目摘要

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.

概括计算生物学正日益成为生物科学研究不可或缺的一部分技术进步提高了调查人员触手可及的数据的能力和深度。计算生物学和生物信息学资源对于本 P01 以 RNA 为中心的目标更为重要。在之前的项目期间，Core B致力于提供有效且及时的计算生物学和为 P01 研究人员提供生物信息学服务，除了 Core 之外，还发表了 11 篇与 Core B 相关的出版物。 B 致力于提高能力和效率，它提供了满足项目特定需求的定制分析软件，并为初级 P01 研究人员提供计算生物学和生物信息学培训，特别是核心 B。通过减少 RNA-seq、ATAC-seq 和 ChIP-seq 标准分析流程的数据处理时间开发在杜兰大学运行的自动化综合分析软件佛罗里达大学高性能计算机 (HPC) 集群大大减少了主要数据。到解释时代，其综合性为 P01 人员提供了很高的价值。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其他任务，例如在上一个项目期间开发新的计算方法和教学。期间，Core B还针对项目1、2的需求，开发了7个以上的软件包 3.最后，核心B采用多管齐下的方式对初级P01调查员进行培训，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优势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。