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，包括模型构建器，可视化工具和教学界面。转录调控是一种复杂的系统行为，它是由许多调节分子与DNA相互作用而产生的。越来越多的证据表明，转录过程的反应不仅仅来自单个组件的变化，而是组件之间的集体行为。该模型构建器将联合收割机将单个分子相互作用的丰富实验数据和转录调控机制的当前模型组合成一个单一的模型，该模型可以模拟沿着DNA的所有分子相互作用沿着。可视化工具将利用各种图形方法（包括动画，图表和图形）来促进对细胞调节转录所用不同机制的随机性的理解。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、探索和发现不同调节机制如何结合联合收割机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理解转录调控的随机性和动态性，并允许探索扰动对不同调控机制的影响。 该项目促进了计算机科学、分子生物学和数学建模领域教师和学生的跨学科研究和培训。这项工作整合到现有的模拟为基础的教育举措和教育推广活动的大学科罗拉多校园。这个项目允许一个博士后，一个研究生，几个本科生，和一些有才华的当地高中学生在一个跨学科的主题的培训。学生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。本科生培训将直接融入项目。所有软件工具和教育材料都将作为开源软件提供。

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.