Modeling transcription

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.

The Summer 2014 Vizualization Group

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This project funded by NSF's Division of Biological Infrastructure
Award #: 1262410

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