Platform and portal development for accessible, reproducible cancer genomics research

用于可访问、可重复的癌症基因组学研究的平台和门户开发

• 批准号: 10460150
• 负责人: John Theodore Liefeld
• 金额: $ 21.11万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-12 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10460150
• 关键词: Achievement; Architecture; Bioinformatics; Cancer cell line; Code; Communities; Computer software; Data; Databases; Development; Educational Activities; Encyclopedias; Funding; Gene set enrichment analysis; Genes; Genomics; Leadership; Malignant Neoplasms; Maps; Methods; Molecular Profiling; Pathway interactions; Reproducibility; Research; Research Activity; Research Personnel; Resources; Scientist; Software Tools; Specialist; The Cancer Genome Atlas; Visualization; anticancer research; base; bioinformatics tool; cancer genomics; design; distributed data; genomic data; interoperability; online resource; open data; open source; outreach; tool; treatment response

Abstract Ted Liefeld is an accomplished software architect and bioinformatics programmer at UCSD who contributes to many cancer research activities in the lab of Unit Director Jill Mesirov. Over the past 20 years, he has developed bioinformatics software tools for reproducible cancer research and open science, as well as numerous cancer analysis and visualization portals and online resources. He has provided architectural and project leadership on: (1) GenePattern, a genomic analysis platform enabling access to hundreds of genomic analysis tools for users at all levels of computational sophistication from nonprogramming investigators to accomplished coding bioinformatic scientists; (2) Gene Set Enrichment Analysis/Molecular Signatures Database (GSEA/MSigDB), used for identifying coordinately regulated sets of genes and activated pathways in genomic data; (3) the design of numerous cancer portals for distributing data from cancer projects including the Cancer Cell Line Encyclopedia, Cancer Therapeutics Response Portal, Project Achilles Portal, Differentiation Map Portal, and TCGA Tumorscape. Mr. Liefeld will use the provided funds for (1) designing and developing new software architectures promoting interoperability of diverse bioinformatics tools and enabling reproducible research; (2) making advanced, compute-intensive cancer bioinformatics methods available to researchers in the worldwide oncogenomics community; (3) developing accessible portals for NCI-funded cancer projects; (4) supporting the cancer research community through outreach and educational activities and initiatives. Based on his past achievements in cancer bioinformatics, open science, and reproducible research, we believe Mr. Liefeld will continue to make essential contributions as an NCI Cancer Research Specialist.

摘要 Ted Liefeld是加州大学圣地亚哥分校颇有成就的软件架构师和生物信息学程序员，他的贡献 在单位主任吉尔·梅西罗夫的实验室里进行了许多癌症研究活动。在过去的20年里，他发展了 生物信息学软件工具，用于可重复的癌症研究和开放科学，以及许多癌症 分析和可视化门户以及在线资源。他在以下方面提供了架构和项目领导： (1)基因组分析平台GenePattern，可为用户提供数百种基因组分析工具 在从非编程研究人员到完成编码的所有计算复杂程度上 生物信息学科学家；(2)基因集浓缩分析/分子签名数据库(GSEA/MSigDB)， 用于识别基因组数据中协调调控的基因和激活途径；(3)设计 众多癌症门户网站，用于发布癌症项目的数据，包括癌细胞系 百科全书，癌症治疗反应门户，阿喀琉斯计划门户，分化地图门户，以及 TCGA Tumorscape。 Liefeld先生将使用所提供的资金(1)设计和开发新的软件架构，以促进 多种生物信息学工具的互操作性和可重复性研究；(2)使先进的， 全球肿瘤基因组学研究人员可用的计算密集型癌症生物信息学方法 社区；(3)为NCI资助的癌症项目开发可访问的门户网站；(4)支持癌症研究 通过外展和教育活动及倡议促进社区发展。基于他过去在癌症方面的成就 生物信息学、开放科学和可重复的研究，我们相信利费尔德先生将继续使 作为NCI癌症研究专家做出的贡献。