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

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是一个开源软件平台，用于生物网络分析，可视化和建模。是 学术界和工业界的重要生物信息学资源，每年下载量超过300，000次， 引用。Cytoscape的广泛采用主要是由于其在各种生物分析中的实用性， 可持续的开放式开发模式及其可扩展的架构，使任何人都可以添加算法 该功能吸引了数百名第三方开发人员。 现在，在网络知识和 概念对基因组学研究越来越重要。Cytoscape在解决这一问题方面处于非常有利的地位 需要并作为基于知识的基因组分析的中心。在此应用程序中，为了支持Cytoscape作为 U24基因组社区资源，我们将努力实现四个具体目标。首先，我们将保持我们的 长期实质性的承诺，生产Cytoscape软件作为一个关键的研究资源。二是 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， 关键的网络生物学工具对生物医学研究人员来说更容易获得， 生物医学数据集和云计算环境中的互操作。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AnVIL、BioData Catalyst和Cancer Genomic Data Commons。第三，我们将共同努力 与外部工具开发商合作，推广一系列用于基于网络的基因组分析的领先工具， 包括数据科学界现有的和新出现的方法。最后我们将 继续提供丰富的Cytoscape培训计划，包括积极引导用户的新材料 通过分析工作流，根据他们提供的输入更新内容。 总之，这些活动不仅将支持Cytoscape资源的生产，还将创建下一个 这是一个基于桌面、网络和云的生态系统，用于在基因组数据科学中使用知识网络。