ABI Innovation: Stochastic Transcription Regulatory Mechanisms - Model building, simulation, and visualization

ABI 创新：随机转录调节机制 - 模型构建、模拟和可视化

• 批准号: 1262410
• 负责人: Robin Dowell
• 金额: $ 68.98万
• 依托单位: University of Colorado at Boulder
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2017-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1262410&HistoricalAwards=false
• 关键词: ABI; Innovation; Stochastic; Transcription; Regulatory

The goal of the project is to construct an integrated transcriptional regulation modeling toolbox composed of a model builder, visualization tools, and a teaching interface. Transcriptional regulation is the complex system behavior that arises from the interaction of numerous regulator molecules with the DNA. There is growing evidence that response of the transcriptional process emerges not solely from the changes in individual components, but rather by the collective behavior between the components. The model builder will combine the abundant experimental data on individual molecule interactions and the current models of transcriptional regulation mechanisms into a single model that can simulate all the molecular interactions along the DNA. The visualization tool will utilize assorted graphical methods (including animations, charts, and graphs) to facilitate the understanding of the random nature of the different mechanisms used by the cell to regulate transcription. And finally, the teaching interface will merge the simulation and visualization components to provide students, educators, and scientists with the ability to experiment, explore, and discover how different regulation mechanisms combine to achieve specific cellular responses. These tools will aid students and researchers in understanding the stochastic and dynamic nature of transcriptional regulation and allow exploration of the effects of perturbation on different regulation mechanisms. This project promotes interdisciplinary research and training among faculty and students in computer science, molecular biology, and mathematical modeling. The work integrates into existing simulation based educational initiatives and educational outreach activities on the University of Colorado campus. This project allows for the training of a postdoc, a graduate student, several undergraduates, and a few talented local high school students in an interdisciplinary topic. Students will be recruited from under-represented populations through the Summer Multicultural Access to Research Training (SMART) and Colorado Diversity Initiative (CDI). Undergraduate student training will be directly integrated into the project. All software tools and educational materials will be publically available as open source.

该项目的目的是构建由模型构建器，可视化工具和教学接口组成的集成转录调节建模工具箱。转录调控是由许多调节剂分子与DNA的相互作用产生的复杂系统行为。越来越多的证据表明，转录过程的响应不仅来自单个组件的变化，而是由于组件之间的集体行为而出现。模型构建器将结合有关单个分子相互作用的丰富实验数据，以及当前的转录调控机制模型中的单个模型，该模型可以模拟沿DNA的所有分子相互作用。可视化工具将利用各种图形方法（包括动画，图表和图形）来促进对单元使用的不同机制来调节转录的随机性的理解。最后，教学界面将合并模拟和可视化组件，以使学生，教育者和科学家能够实验，探索和发现不同调节机制如何结合以实现特定的细胞响应。这些工具将帮助学生和研究人员了解转录调控的随机和动态性质，并允许探索扰动对不同调节机制的影响。 该项目促进了计算机科学，分子生物学和数学建模的教师和学生之间的跨学科研究和培训。这项工作融入了科罗拉多大学校园的现有基于模拟的教育计划和教育外展活动。该项目允许培训博士后，研究生，几个本科生以及一些跨学科主题的当地高中生。通过夏季多元文化访问研究培训（SMART）和科罗拉多州多样性计划（CDI），将从代表性不足的人群中招募学生。本科生培训将直接纳入项目。所有软件工具和教育材料都将公开作为开源。