Core--Genomics and Bioinformatics

核心——基因组学与生物信息学

• 批准号: 7600606
• 负责人: PETER Karl SORGER
• 金额: $ 31.93万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 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/7600606
• 关键词: Animal Model; Antibiotics; Architecture; Arts; Binding; Bioinformatics; Biological; Biological Assay; Biology; Chemicals; Chemistry; Client; Collaborations; Computer software; Computers; Computing Methodologies; Condition; Copper; Core Facility; Custom; DNA; DNA Damage; DNA lesion; Data; Data Analyses; Data Storage and Retrieval; Database Management Systems; Databases; Deoxyribose; Development; Devices; Dose; Ecology; Educational process of instructing; Engineering; Ensure; Environment; Environmental Health; Fees; Foundations; Funding; Genes; Genome; Genomics; Goals; Housing; Human; Individual; Information Systems; Information Technology; Iron; Joints; Laboratories; Licensing; Link; Linux; Messenger RNA; Microarray Analysis; Mining; Minor Groove; Modeling; Modification; NCI Center for Cancer Research; Nitrogen; Numbers; Oceans; Oligonucleotides; Operative Surgical Procedures; Organism; Oxidants; Pathology; Personal Satisfaction; Phosphorus; Photosynthesis; Pliability; Positioning Attribute; Procedures; Process; Prochlorococcus; Protein Array; Proteins; Protocols documentation; Purpose; Quality Control; Radiation; Research; Research Personnel; Resources; Saccharomyces cerevisiae; Services; Signal Transduction; Site; Software Tools; Solar Energy; Spottings; System; Techniques; Technology; Training; Whole Organism; Work; Yeasts; Zinostatin; analytical method; base; cDNA Arrays; carbon fixation; computer data analysis; data mining; data modeling; design; ds-DNA; interest; large-scale database; member; microorganism; new technology; open source; oxidation; programs; response; software systems; technology development; tool

The Genomics and Bioinformatics Facilities Core was created in September 2001 to provide Center members with integrated facilities for microarray fabrication, microarray analysis, database storage, large-scale database management, data mining and data modeling. The Core is comprised of the CEHS Bioinformatics Computing Facility tightly integrated with the MIT BioMicro Center. The latter is a joint endeavor of the Center for Environmental Health Sciences, the Department of Biology, the Center for Cancer Research, and Biological Engineering Division that was founded in 2000 as the central bio-fabrication and bio-information technology resource at MIT. The specific aims of the Genomies and Bioinformatics Facilities Core are: (1) To provide integrated support for both commercial and custom microarrays. The Core will support the fabrication of spotted oligo arrays and spotted cDNA arrays when commercially available arrays are not available. The Core will also support the use of Affymetrix GeneChips and Agilent microarrays providing flexibility with enabled comparisons and are immensely valuable for studies where whole-genome coverage is needed. Though the current focus of most Center members is on mRNA analysis, the capabilities of the Core can be extended to the fabrication and analysis of other types of arrays including protein arrays. (2) To provide strong three-tier architecture for data storage, management and processing. The Core has installed several three-tier client-server systems based on open-source and commercial database management systems (DBMS). These systems will be strengthened and extended to achieve integrated support for GeneChips and spotted microarrays. (3) To provide networks of managed desktop computers for data analysis and mining. The Core has licensed commercial software such as the Affymetrix MicroArray Suite-DataMiningTools suite and Spotfire Decision Site for microarray data analysis. The number of licenses will be increased and open-source tools integrated into the 3-tier Core IT system. Client software will be deployed on a network of managed desktop computers based on the MIT Win-Athena, Windows 2000 and Linux-Athena environments. (4) To provide training and educational programs in commercial and open-source bioinformatics software. A program of professional training seminars for commercial software will be strengthened and supplemented with seminars taught in-house for open-source software. Center investigators will have free access to training sessions that are usually fee-based. (5) To provide Center members with technical assistance with programming, database administration and data analysis. Bioinformatics applications that currently operate separately from each other will be integrated. (6) To work with Center members in applying their results to the development of data models and quality control procedures, error modeling as well as the development of new technologies. The introduction of new devices and computational methods will be accelerated through close collaborations between Center members and other researchers at MIT. The Center maintains a strong commitment to new technology development and deployment. A focus on new technology also helps to ensure that the Genomics and Bioinformatics Facilities Core remains at the cutting edge of high throughput analytical methods.

基因组学和生物信息学设施核心于2001年9月创建，为中心成员提供微阵列制造、微阵列分析、数据库存储、大规模数据库管理、数据挖掘和数据建模的综合设施。该核心由与麻省理工学院生物微中心紧密集成的 CEHS 生物信息学计算设施组成。后者是环境健康科学中心、生物系、癌症研究中心和生物工程部门的共同努力，该部门成立于 2000 年，是麻省理工学院的中央生物制造和生物信息技术资源。基因组和生物信息学设施核心的具体目标是：（1）为商业和定制微阵列提供综合支持。核心将支持 当没有市售阵列时，可以制造点状寡核苷酸阵列和点状 cDNA 阵列。该核心还将支持 Affymetrix GeneChips 和 Agilent 微阵列的使用，提供可进行比较的灵活性，对于需要全基因组覆盖的研究非常有价值。尽管大多数中心成员当前的重点是 mRNA 分析，但 Core 的功能可以扩展到其他类型阵列（包括蛋白质阵列）的制造和分析。 (2)为数据存储、管理和处理提供强大的三层架构。 Core 安装了多个基于开源和商业数据库管理系统 (DBMS) 的三层客户端-服务器系统。这些系统将得到加强和扩展，以实现一体化 支持 GeneChips 和斑点微阵列。 (3) 提供托管桌面计算机网络，用于数据分析和挖掘。 Core 已获得许可的商业软件，例如用于微阵列数据分析的 Affymetrix MicroArray Suite-DataMiningTools 套件和 Spotfire Decision Site。许可证数量将增加，开源工具将集成到三层核心 IT 系统中。客户端软件将部署在基于 MIT Win-Athena、Windows 2000 和 Linux-Athena 环境的托管桌面计算机网络上。 (4) 提供商业和开源生物信息学软件的培训和教育计划。商业软件专业培训研讨会计划将得到加强，并辅之以内部教授的开源软件研讨会。中心调查员可以免费参加通常收费的培训课程。 (5) 为中心成员提供编程、数据库管理和数据分析方面的技术援助。目前彼此独立运行的生物信息学应用程序将被整合。 (6) 与中心成员合作，将其成果应用于数据模型和质量控制程序的开发、错误建模以及新技术的开发。通过中心成员和麻省理工学院其他研究人员之间的密切合作，将加速新设备和计算方法的引入。该中心坚定致力于新技术的开发和部署。对新技术的关注也有助于确保基因组学和 生物信息学设施核心仍然处于高通量分析方法的前沿。