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

该项目的目标是构建一个集成的转录调控建模工具箱，由模型构建器、可视化工具和教学界面组成。转录调控是一种复杂的系统行为，由众多调控分子与DNA相互作用而产生。越来越多的证据表明，转录过程的反应不仅来自单个成分的变化，而且来自成分之间的集体行为。模型构建器将把关于单个分子相互作用的丰富实验数据和目前转录调控机制的模型结合到一个模型中，该模型可以模拟DNA沿线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)来帮助理解细胞用来调节转录的不同机制的随机性质。最后，教学界面将合并模拟和可视化组件，为学生、教育工作者和科学家提供实验、探索和发现不同调控机制如何组合以实现特定细胞响应的能力。这些工具将帮助学生和研究人员理解转录调控的随机和动态性质，并允许探索扰动对不同调控机制的影响。该项目促进了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倡议和教育推广活动。这个项目允许培养一名博士后，一名研究生，几名本科生，以及几名有才华的当地高中生，在一个跨学科的主题。将通过夏季多元文化获取研究培训(SMART)和科罗拉多州多样性倡议(CDI)从代表性不足的人群中招收学生。本科生培养将直接融入该项目。所有软件工具和教育材料都将作为开放源码公开提供。

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.