Aim 1:
Conduct transdisciplinary research to advance our ability to represent cellular and tissue processes mathematically and explain how drugs perturb these processes. For this we will create and analyze a cluster of models across scales to study the dynamic topology of regulatory networks and how information processing within the network results in cellular behaviors that propagate across scales to yield tissue and organ behavior. We will study on the role of components that are drug targets and participants in regulatory network motifs to understand how drug interactions with these components lead to reconfiguration of network motifs and altered physiology.
Aim 2:Continue the development of a large-scale database of direct mammalian interactions. We will develop novel tools to construct, analyze and visualize networks and network motifs at various scales of organization. These tools will range from desktop applications and web-based tools databases, and programs for massively parallel computing using clusters of 1000 nodes or more (e.g. IBM BlueGene). We will develop parallel programs for computing deterministic and hybrid models for large (>1000 components) networks.
Aim 3:Continue the development and implementation of multivariable experiments at the proteomic and genomic levels.
Aim 4:Develop a novel curriculum that can be used for the teaching of systems biology of physiology, pathophysiology and pharmacology. The centerpiece of this program will be an integrated course that will use selected examples in a problem-based interactive learning format to cover cellular regulatory systems, physiology, pharmacology, and mathematical modeling across scales. This course will lead to customized mini-workshops for individualized training, which in turn lead to feasibility projects that will be connected to the Center and funded by it. Flexible entry at each stage will be available. The integrated training will be broad-based, with components focused on graduate students, postdoctoral fellows, and other investigators including PIs and educators who teach both undergraduate and graduate courses.
Aim 5:Develop and conduct workshops and symposia geared towards the introduction of systems biology approaches into ongoing research projects in the experimental laboratories or foster the training of physical and mathematical scientists in experimental techniques used in Systems Biology research. These events will be open to all.
Aim 6:Introduce senior undergraduate students to research in Systems Biology by funding and developing summer undergraduate internships, in conjunction with the Biomedical Engineering Program of CCNY and the colleges of the CUNY system. There will be special emphasis on attracting under-represented minority students to this program.
Overall Strategy for Integration of Modeling and Experiments in SBCNY