CYTOSCAPE: AN ECOSYSTEM FOR NETWORK GENOMICS

CYTOSCAPE：网络基因组学的生态系统

• 批准号: 10411738
• 负责人: Trey Ideker
• 金额: $ 154.31万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10411738
• 关键词: Academia; Address; Adoption; Algorithms; Architecture; Attention; Biological; Biological Markers; Biological Process; Biology; Cloud Computing; Communities; Computer software; Data; Data Science; Data Set; Development; Disease; Drug Targeting; Ecosystem; Environment; Extramural Activities; Funding; Gene Expression; Generations; Genetic Heterogeneity; Genetic Variation; Genomic Data Commons; Genomics; Genotype-Tissue Expression Project; Grant; Human Genome; Industry; Internet; Investments; Knowledge; Maintenance; Modeling; Molecular; Mutation; Network-based; Online Systems; Pathway Analysis; Pathway interactions; Phenotype; Positioning Attribute; Production; Research; Research Personnel; Resources; Services; System; The Cancer Genome Atlas; Time; Training Programs; Training Support; United States National Institutes of Health; Untranslated RNA; Update; Variant; Visualization; Work; base; bioinformatics resource; cancer genome; cancer genomics; catalyst; cloud based; gene regulatory network; genetic variant; genome analysis; genome sequencing; genomic data; infancy; innovation; knowledge base; knowledge hub; large datasets; model development; multiple omics; next generation; open source; software infrastructure; tool; tumor heterogeneity; Academia; Address; Adoption; Algorithms; Architecture; Attention; Biological; Biological Markers; Biological Process; Biology; Cloud Computing; Communities; Computer software; Data; Data Science; Data Set; Development; Disease; Drug Targeting; Ecosystem; Environment; Extramural Activities; Funding; Gene Expression; Generations; Genetic Heterogeneity; Genetic Variation; Genomic Data Commons; Genomics; Genotype-Tissue Expression Project; Grant; Human Genome; Industry; Internet; Investments; Knowledge; Maintenance; Modeling; Molecular; Mutation; Network-based; Online Systems; Pathway Analysis; Pathway interactions; Phenotype; Positioning Attribute; Production; Research; Research Personnel; Resources; Services; System; The Cancer Genome Atlas; Time; Training Programs; Training Support; United States National Institutes of Health; Untranslated RNA; Update; Variant; Visualization; Work; base; bioinformatics resource; cancer genome; cancer genomics; catalyst; cloud based; gene regulatory network; genetic variant; genome analysis; genome sequencing; genomic data; infancy; innovation; knowledge base; knowledge hub; large datasets; model development; multiple omics; next generation; open source; software infrastructure; tool; tumor heterogeneity

CYTOSCAPE: AN ECOSYSTEM FOR NETWORK GENOMICS PROJECT SUMMARY Cytoscape is an open source software platform for biological network analysis, visualization and modeling. It is a critical bioinformatics resource in academia and industry, with 300,000+ downloads per year and 25,000+ citations. The widespread adoption of Cytoscape is due mainly to its utility in diverse biological analyses, its sustainable open development model, and its extensible architecture, which enables anyone to add algorithmic functionality and has attracted hundreds of third-party developers. Access to network analysis tools is particularly important now, at a time when network knowledge and concepts are increasingly central to genomics research. Cytoscape is in an excellent position to address this need and serve as a hub for knowledge-based genome analysis. In this application to support Cytoscape as a U24 Genomic Community Resource, we will work towards four specific aims. First, we will maintain our longtime substantial commitment to produce Cytoscape software as a critical research resource. Second, we will complete our ongoing development of Cytoscape as an ecosystem of tools and services on the web, so that key network biology tools are more accessible to biomedical researchers and can readily access big biomedical datasets and interoperate in cloud computing environments. Immediate targets of these developments will be resources in which federal organizations are already making substantial investments, including AnVIL, BioData Catalyst and Cancer Genomic Data Commons. Third, we will work collaboratively with outside tool developers to promote a constellation of leading tools for network-based genomic analysis, including both existing and nascent approaches emerging from the data science community. Finally, we will continue to offer a rich set of Cytoscape training programs, including new material that actively guides users through analysis workflows, updating content based on input they provide. In summary, these activities will support not only production of the Cytoscape resource– they will create a next generation desktop, web and cloud-based ecosystem for using knowledge networks in genomic data science.

Cytoscape：网络基因组学的生态系统 项目摘要 Cytoscape是用于生物网络分析，可视化和建模的开源软件平台。这是 学术界和行业中的重要生物信息学资源，每年下载300,000多个和25,000多个 引用。 Cytoscape的宽度采用主要是由于其在潜水员生物学分析中的效用， 可持续开放开发模型及其可扩展的体系结构，使任何人都可以添加算法 功能，吸引了数百个第三方开发人员。 在网络知识和 概念对基因组学研究越来越核心。 Cytoscape在解决这个问题上处于一个很好的位置 需要并充当基于知识的基因组分析的枢纽。在此应用程序中，以支持细胞施加 U24基因组社区资源，我们将致力于四个特定目标。首先，我们将维护我们的 长期致力于生产Cytoscape软件作为关键研究资源。第二，我们 将完成我们正在进行的Cytoscape开发，作为网络上工具和服务的生态系统，因此 生物医学研究人员更容易获得该关键网络生物学工具，并且可以很容易地访问 生物医学数据集并在云计算环境中进行互操作。这些的直接目标 发展将是联邦组织已经进行大量投资的资源， 包括砧，生物催化剂和癌症基因组数据共享。第三，我们将协作工作 借助外部工具开发人员来促进用于基于网络的基因组分析的领先工具的星座， 包括数据科学界出现的现有和新生方法。最后，我们会的 继续提供丰富的Cytoscape培训计划，包括积极指导用户的新材料 通过分析工作流程，根据他们提供的输入来更新内容。 总而言之，这些活动不仅将支持Cytoscape资源的生产 - 它们将创建下一个 一代台式机，基于Web和云的生态系统，用于在基因组数据科学中使用知识网络。