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.

该项目的目标是构建一个由模型构建器、可视化工具和教学界面组成的集成转录调控建模工具箱。转录调控是由众多调控分子与 DNA 相互作用而产生的复杂系统行为。越来越多的证据表明，转录过程的反应不仅来自于单个成分的变化，还来自于成分之间的集体行为。模型构建器将把有关单个分子相互作用的丰富实验数据和当前的转录调控机制模型结合到一个模型中，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、图表和图表）来帮助理解细胞用于调节转录的不同机制的随机性质。最后，教学界面将融合模拟和可视化组件，为学生、教育工作者和科学家提供实验、探索和发现不同调节机制如何结合以实现特定细胞反应的能力。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本质，并允许探索扰动对不同调控机制的影响。 该项目促进教师和学生在计算机科学、分子生物学和数学建模方面的跨学科研究和培训。这项工作融入了科罗拉多大学校园现有的基于模拟的教育计划和教育外展活动。该项目可以对一名博士后、一名研究生、几名本科生和一些有才华的当地高中生进行跨学科主题的培训。将通过夏季多元文化研究培训（SMART）和科罗拉多多样性倡议（CDI）从代表性不足的人群中招募学生。本科生培养将直接纳入该项目。所有软件工具和教育材料都将以开源形式公开提供。