Cytoscape: A Modeling Platform for Biomolecular Networks

Cytoscape：生物分子网络建模平台

基本信息

批准号：
7240435
负责人：
Trey Ideker
金额：
$ 46.28万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2004
资助国家：
美国
起止时间：
2004-06-01 至 2009-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7240435
关键词：
Address Algorithms Architecture Autacoids Automobile Driving Basic Science Binding Biochemical Pathway Bioinformatics Biological Biological Markers Biological databases California Cell model Cell physiology Cells Chemical Models Classification Code Collaborations Communication Communities Complex Computational Biology Computer Simulation Computer software Data Databases Development Disease Documentation Drug Delivery Systems Engineering Ensure Evolution Facility Construction Funding Category Funding Genome Goals Imagery Industry Institutes Institution Internet Kinetics Laboratories Libraries Literature Maintenance Maps Measurement Measures Memorial Sloan-Kettering Cancer Center Modeling Molecular Molecular Biology Molecular Profiling Network-based Numbers Operative Surgical Procedures Pathway interactions Phenotype Plug-in Process Proteins Range Reading Research Project Grants Services Software Engineering Speed Standards of Weights and Measures Systems Biology Technology Testing Thumb structure Time Universities Writing base biological research design graphical user interface microbial alkaline proteinase inhibitor models and simulation network models open source programs reaction rate repository research and development simulation software development success tool

项目摘要

DESCRIPTION (provided by applicant): Cytoscape is an Open Source software project for integrating biomolecular interaction networks with genome-scale expression data and other molecular states into a unified conceptual framework. The software is built and maintained by a cross-disciplinary and cross-institutional collaboration, expanding over the past several years to include groups at the University of California San Diego, the Institute for Systems Biology, and the Computational Biology Center at Memorial Sloan-Kettering Cancer Center. We propose an aggressive program of research and development for expanding the current code base, including improvements to the Cytoscape core architecture and user interface; construction of a data services layer with direct access to multiple biological databases hosted on the Internet; and, to extend Cytoscape's applicability to a broader biological research community, a substantial increase in the number of publicly available plug-in analyses. Equally as important, we plan rigorous measures to bolster and maintain existing features, including a library of software unit tests; design rules of thumb; timely and thorough documentation and release of new versions; and community open-source support. In so doing, Cytoscape promises to become an integrated and accessible entry-point into the large amount of molecular interaction data now being generated. Moreover, through computational modeling of biomolecular interaction networks, Cytoscape will be a key enabling technology towards one of the ultimate goals of systems biology: to draft and map the complete high-level 'wiring diagram' of molecular interactions driving cellular physiology, evolution, and disease; and to interface this wiring diagram to lower level physico-chemical models of the cell.

描述（由申请人提供）：Cytoscape是一个开源软件项目，用于将生物分子相互作用网络与基因组尺度表达数据和其他分子状态整合到统一的概念框架中。该软件是由跨学科和跨机构合作构建和维护的，在过去的几年中不断扩展，以包括加州大学圣地亚哥分校，系统生物学研究所以及纪念斯隆 - 凯特特林癌症中心的计算生物学中心的小组。我们提出了一个积极的研发计划，以扩大当前代码基础，包括改进Cytoscape核心体系结构和用户界面；构建数据服务层，直接访问Internet上托管的多个生物数据库；并且，为了将Cytoscape的适用性扩展到更广泛的生物学研究界，可公开可用的插件分析数量大大增加。同样重要的是，我们计划采取严格的措施来加强和维护现有功能，包括软件单元测试库；经验设计规则；及时，详尽的文档和新版本的发布；和社区开源支持。这样一来，Cytoscape承诺将成为现在生成大量分子相互作用数据的集成且可访问的入口点。此外，通过对生物分子相互作用网络的计算建模，Cytoscape将是实现系统生物学最终目标之一的关键技术：草拟和绘制驱动细胞生理学，进化和疾病的完整高级“接线图”的完整高级“接线图”；并将此接线图连接到细胞的较低水平的理化模型。