Cytoscape: A Modeling Platform for Biomolecular Networks

Cytoscape：生物分子网络建模平台

• 批准号: 10415596
• 负责人: Trey Ideker
• 金额: $ 58.63万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-15 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10415596
• 关键词: Academia; Address; Administrative Supplement; Adopted; Algorithms; Architecture; Award; Biological; Biological Markers; Budgets; California; Communities; Computer software; Development; Disease; Drug Targeting; Ecosystem; Funding; Genomics; Grant; Industry; Knowledge; Maintenance; Modeling; Molecular; Online Systems; Pathway Analysis; Pathway interactions; Research; Research Personnel; Resources; Time; Training Programs; United States National Institutes of Health; Universities; Update; Visualization; base; bioinformatics resource; cloud based; cost; genetic variant; genome analysis; knowledge base; knowledge hub; model development; open source; outreach program; tool

CYTOSCAPE: A MODELING PLATFORM FOR BIOMOLECULAR NETWORKS Administrative supplement request to extend R01 HG009979 for a period of one year (7/1/21 to 6/30/22) PI: Trey Ideker (University of California San Diego) 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. Cytoscape has been widely adopted 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 addresses this need and serves as a hub for knowledge-based genome analysis. Here in this administrative supplement application, we are requesting additional funds to permit a one-year extension to the budget period of the current grant (R01 HG009979). These bridge funds will enable continued maintenance and dissemination of the Cytoscape ecosystem of tools while our U24 Genomic Community Resource application is still under review (U24 HG012107, resubmission May 25, 2021). The requested $586K in total costs is a reduction from the current award and the base amount required to maintain, support and incrementally update the widely used Cytoscape platform during the intervening period. These funds will also serve to retain our highly specialized Cytoscape development team. With this one-year supplemental funding request, we propose to: 1. Continue our longtime commitment to maintain, update and distribute the Cytoscape ecosystem of tools. 2. Further develop a web- and cloud-based version of Cytoscape, Cytoscape Explore, and release v1.0 with basic Cytoscape Desktop functionality. 3. Continue our rich set of Cytoscape outreach and training programs.

Cytoscape：生物分子网络建模平台 将R01 HG009979延长一年的行政补充请求（21年7月1日至22年6月30日） PI：Trey Ideker（加州圣地亚哥大学） 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已被广泛采用，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。访问网络分析工具是 尤其重要的是，在网络知识和概念日益成为 基因组学研究Cytoscape满足了这一需求，并作为基于知识的基因组的中心 分析. 在这份行政补充申请中，我们要求额外的资金， 延长当前赠款的预算期（R01 HG009979）。这些过渡基金将使 维护和传播Cytoscape生态系统的工具，而我们的U24基因组社区 资源申请仍在审查中（U24 HG012107，2021年5月25日重新提交）。要求的586K美元 在总费用中，是从目前的裁定额和维持、支持和 在此期间逐步更新广泛使用的Cytoscape平台。这些基金还将 保留我们高度专业化的Cytoscape开发团队。 通过这一为期一年的补充资金申请，我们建议： 1.继续我们的长期承诺，维护，更新和分发Cytoscape工具生态系统。 2.进一步开发基于Web和云的Cytoscape版本，Cytoscape Explore，并发布v1.0， 基本的Cytoscape桌面功能。 3.继续我们丰富的Cytoscape推广和培训计划。

项目成果

Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis

• DOI: 10.1016/j.isci.2019.08.057
• 发表时间: 2019-09
• 期刊: iScience
• 影响因子: 5.8
• 作者: M. T. Moutaoufik;Ramy H. Malty;S. Amin;Qingzhou Zhang;S. Phanse;Alla Gagarinova;Mara Zilocchi;Larissa Hoell;Z. Minić;M. Gagarinova;H. Aoki;J. Stockwell;M. Jessulat;Florian Goebels;Kirsten Broderick;Nichollas E. Scott;James Vlasblom;Gabriel Musso;B. Prasad;E. Lamantea;B. Garavaglia;A. Rajput;K. Murayama;Y. Okazaki;L. Foster;Gary D Bader;F. Cayabyab;M. Babu

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.

系统与合成生物学标准规范：2019年现状与发展。

• DOI: 10.1515/jib-2019-0035
• 发表时间: 2019
• 期刊: Journal of integrative bioinformatics
• 影响因子: 1.9
• 作者: Schreiber,Falk;Sommer,Björn;Bader,GaryD;Gleeson,Padraig;Golebiewski,Martin;Hucka,Michael;Keating,SarahM;König,Matthias;Myers,Chris;Nickerson,David;Waltemath,Dagmar
• 通讯作者: Waltemath,Dagmar