Computational Biology Core

计算生物学核心

• 批准号: 7649744
• 负责人: HAROLD R GARNER
• 金额: $ 36.04万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-03-01 至 2009-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7649744
• 关键词: Bioinformatics; Biological; Categories; Code; Collaborations; Collection; Communities; Computational Biology; Computers; Custom; DNA Microarray Chip; DNA Resequencing; Data; Data Analyses; Data Set; Databases; Development; Environment; Experimental Designs; Funding; Genomics; Grant; Human Resources; Internet; Literature; Methods; Oligonucleotide Probes; Open Reading Frames; Performance; Polymerase Chain Reaction; Proteomics; Publications; Reporting; Research; Research Personnel; Resources; Sampling; Scientist; Security; Services; Solutions; Speed; System; Technology; Testing; Text; Work; base; biothreat; computer code; data acquisition; pathogen; programs; response; tool

Bioinformatics tools, custom databases, experimental designs, data acquisition/archival/access methods and data analysis/interpretation methods have had and will continue to have great impact on the RCE progress and will be the deliverables of a bioinformatics program. It should be noted that new bioinformatics technologies are anticipated to be developed and they will be necessary to integrate and analyze the many diverse types of data, and ideas for these tools will come from the biological scientists working in the projects and cores as well as bioinformaticists in our core, but bioinformaticists will develop the solution. We also leverage the existing commercial and non-commercial systems (tools, databases, development environments) to speed the bioinformatics solution development, for maximum data exchange compatibility issues, such as security, and for robustness. In the previous grant period, we created numerous tools and databases, which have had tens of thousands of users, have analyzed over 25 large array-based datasets and have reported this work in 13 publications. The Specific Aims for this core are: 1) To develop applied computational biology resources-codes databases and interpretations of data-to facilitate advances in the understanding and characterization of Category A-C pathogens, validate the performance of the codes/databases either collaboratively or via wet lab testing/checking a sampling of results and to provide computational support for project investigators; 2) To apply our computer codes (new and pathogen adapted) to pre-compute a variety of data for Category A-C pathogens, including ORF amplification primers (PCR, qPCR), DMA chip oligonucleotide probes for re-sequencing and expression, a collection of text-based literature and its extracted and associated biomedical objects: 3) To construct a pathogen-specific, internet accessible, www-based bioinformatics tool set and data warehouse of utilities and make them available to facilitate intra- and inter- institutional collaborations among project and core personnel and others in the biothreat and emerging pathogen research community; 4) To provide an experimental design data analysis and interpretation collaborative service to RCE researchers, especially as it appears to data intensive studies such as pathogen or host expression, proteomics or genomics, and 5) To continue to expand and maintain computer servers to support this effort.

生物信息学工具、定制数据库、实验设计、数据采集/存档/访问方法以及 数据分析/解释方法已经并将继续对RCE的进展产生重大影响 将成为生物信息学项目的成果。值得注意的是，新的生物信息学 预计将开发新的技术，这些技术将有必要集成和分析许多 不同类型的数据，以及这些工具的想法将来自参与项目的生物科学家 以及我们核心的生物信息学家，但生物信息学家将开发解决方案。我们也 利用现有的商业和非商业系统（工具、数据库、开发 环境），以加快生物信息学解决方案的开发，实现最大的数据交换兼容性 问题，例如安全性和鲁棒性。在上一个赠款期间，我们创建了许多工具， 拥有数万用户的数据库已经分析了超过25个大型阵列数据集 并在13份出版物中报告了这项工作。该核心的具体目标是：1）开发应用 计算生物学资源-代码数据库和数据解释-以促进 了解和表征A-C类病原体，验证 合作或通过湿实验室测试/检查结果的抽样，并提供 为项目研究人员提供计算支持; 2）应用我们的计算机代码（新的和病原体 用于预先计算A-C类病原体的各种数据，包括ORF扩增引物 (PCR、qPCR）、用于重测序和表达的DMA芯片寡核苷酸探针、基于文本的聚合物寡核苷酸探针的集合。 文献及其提取和相关的生物医学对象：3）构建病原体特异性， 可访问的、基于万维网的生物信息学工具集和数据仓库，并将其提供给 促进项目和核心人员及其他人员之间的机构内和机构间合作， 生物威胁和新兴病原体研究社区; 4）提供实验设计数据分析 和解释合作服务RCE研究人员，特别是因为它似乎数据密集型研究 如病原体或宿主表达、蛋白质组学或基因组学，以及5）继续扩大和维持 计算机服务器来支持这项工作。