ChemMine Tools: an Open Source Framework for Chemical Genomics

ChemMine Tools：化学基因组学的开源框架

• 批准号: 0957099
• 负责人: Thomas Girke
• 金额: $ 60.1万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-15 至 2015-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0957099&HistoricalAwards=false
• 关键词: ChemMine; Tools; Open; Source; Framework

The University of California, Riverside is awarded a grant to develop ChemMineTools, an environment to efficiently analyze and model large sets of small molecules along with their bioactivity data. It will provide unrestricted access to a scalable set of open source tools that integrates novel and existing algorithm. To maximize its utility spectrum for experimental and computational scientists, the analysis modules will be available from the powerful R environment, as well as an intuitive-to-use web interface. The specific objectives of this project are: (1) The development and implementation of accelerated compound search and clustering algorithms that scale to today's large databases with millions entries. This will focus on the expansion of the ultrafast EI-Search and EI-Clustering algorithms by embedding and indexing (EI). These multipurpose algorithms will be adopted to advanced similarity measures that can currently not be used for processing large databases due their insufficient speed performance. (2) The R package ChemMine R Tools will be developed. It will offer access to advanced clustering, machine learning and visualization functionalities along with interactive visualization tools. (3) User-friendly access to all analysis and visualization tools will be provided by the ChemMine Web Tools interface. (4) An educational outreach program will be offered to provide extensive training opportunities and to integrate underrepresented groups into this project. By integrating novel and existing analysis routines in an efficient data mining environment, the project will disseminate and transform multidisciplinary concepts of powerful chemical approaches in modern biology. Moreover, it will encourage young scientists to incorporate cheminformatics strategies into their daily research. Substantial educational resources for interdisciplinary training at the intersect of computational biology and cheminformatics will be provided by this project. Workshops will be offered to scientists, postdoctoral researchers, graduate, undergraduate, high school and other K-12 students. Members of underrepresented groups will participate in all aspects of this project. Extensive online workshop and software manuals will be provided to maximize the educational outreach of the activities. Further information about this project may be found at its website: http://cmtools.ucr.edu.

加利福尼亚大学河滨分校获得了开发Chemminetools的赠款，这是一个有效分析和建模大型小分子以及其生物活性数据的环境。它将不受限制地访问一组可扩展的开源工具，这些工具集成了新颖和现有算法。为了最大程度地利用实验和计算科学家的实用频谱，分析模块将从强大的R环境以及直观到使用的Web界面中获得。该项目的具体目标是：（1）加速复合搜索和聚类算法的开发和实施，这些算法扩展到当今具有数百万个条目的大型数据库。这将着重于通过嵌入和索引（EI）的超快EI搜索和EI簇算法的扩展。这些多功能算法将用于高级相似性度量，这些算法目前无法用于处理大型数据库，因为它们的速度性能不足。 （2）将开发R包化学R工具。它将提供对高级聚类，机器学习和可视化功能以及交互式可视化工具的访问。 （3）Chemmine Web工具接口将提供对所有分析和可视化工具的用户友好访问。 （4）将提供一项教育外展计划，以提供广泛的培训机会，并将代表性不足的群体整合到该项目中。通过在有效的数据挖掘环境中整合新颖和现有的分析程序，该项目将传播和改变现代生物学强大化学方法的多学科概念。 此外，它将鼓励年轻科学家将化学信息学策略纳入其日常研究。该项目将提供在计算生物学和化学信息学相交的跨学科培训的大量教育资源。讲习班将提供给科学家，博士后研究人员，研究生，本科，高中和其他K-12学生。代表性不足的小组的成员将参与该项目的各个方面。将提供广泛的在线研讨会和软件手册，以最大程度地提高活动的教育宣传。有关该项目的更多信息可以在其网站上找到：http：//cmtools.ucr.edu。