Comparative Approaches to Bio-knowledge Discovery

描述(由申请人提供)：在这项旨在建立生物医学计算卓越计划的规划拨款中，宾夕法尼亚大学和费城儿童医院提议建立一个新的组织，作为生物医学计算研究的中心渠道，将三所学校和六家研究机构的活动联系在一起。该组织将包括一个由内部和外部成员组成的科学指导委员会，以监督研究活动；一个监督委员会，以提供机构支助；一个执行委员会，以管理日常活动；以及一个教育局，以协调培训活动。该组织结构将在宾夕法尼亚大学基因组研究所和宾夕法尼亚大学生物信息学中心的保护伞下产生，以利用现有资源。 将通过资助12个新的种子赠款(通过匹配基金使之成为可能)来促进跨学科研究互动，重点是生物医学知识发现的比较方法。在第一年，将资助四个项目：(1)比较基因组学中的模式发现；(2)计算系统学重建；(3)癌症研究的比较文本挖掘；以及(4)镰状细胞疾病的比较信息学方法。在随后的几年中，将通过内部征求建议书，在前四个项目中增加新的项目。科学指导委员会将审查这些建议，并将在第二年和第三年资助四个新项目。每年都会审查现有项目，并在规划拨款结束时审查所有项目，以便将其合并为少数影响较大的项目。 现有的计算学院和生物医学学院之间的新互动将通过举办机会展示静修会来鼓励，以向来自互补领域的研究人员介绍生物学问题和计算方法。教师基础教育研讨会每月举行一次，其中将以高度互动的形式讨论“转录”等基本概念。现有的生物信息学核心设施将增加额外的高性能计算硬件，支持教授基本计算生物学工具，以及协调根据这笔赠款开发的软件工具的传播。将补充现有的生物医学计算博士水平培训计划，为本科生和硕士学生提供研究经验。

DESCRIPTION (provided by applicant): In this planning grant to establish a Program of Excellence in Biomedical Computing, the University of Pennsylvania and the Children's Hospital of Philadelphia propose to develop a new organization that will serve as a central conduit of biomedical computing research tying together the activities of three schools and six research institutes. The organization will consist of a scientific steering committee with internal and external members to oversee research activities, an oversight committee to provide institutional support, an executive committee to govern day-to-day activities, and an office of education to coordinate the training activities. The organizational structure will be generated under the umbrella of the Penn Genomics Institute and the Penn Center for Bioinformatics to leverage existing resources. Interdisciplinary research interactions will be promoted by funding 12 new seed grants (made possible by matching funds) focusing on comparative approaches to biomedical knowledge discovery. In the first year, four projects will be funded: (1) pattern discovery in comparative genomics; (2) computational phylogeny reconstruction; (3) comparative text mining for cancer research; and (4) comparative informatics approach to sickle-cell disease. In subsequent years, new projects will be added to the first four through an internal solicitation for proposals. The Scientific Steering Committee will review these proposals and four new projects will be funded in Years 2 and 3. Each year, existing projects will be reviewed and at the end of the planning grant, all projects will be reviewed for consolidation into a small number of high impact projects. New interactions between existing computational faculty and biomedical faculty will be encouraged by holding opportunity presentation retreats to introduce researchers from complementary fields to biological problems and computational methods. Faculty basic education seminars will be held monthly where basic concepts like "transcription" will be discussed in a highly interactive format. The existing core facility for bioinformatics will be augmented with additional high-performance computing hardware, support for teaching basic computational biology tools, and a facility to coordinate dissemination of software tools developed from this grant. An existing PhD level training program in biomedical computing will be supplemented to provide research experience for undergraduates and masters students.