Automation of Inferring Biological Network Models

Fall 2013

Chang Sheng Cle Loh
Natasa Miskov-Zivanov
Project description

This project focuses on automating creation and analysis of models of cell signaling networks. These models include several layers of cell signaling: (i) external or receptor layer signaling, (ii) intracellular signaling pathways, and (iii) nuclear or gene regulation signaling. The objective of this project is to create a framework in C/C++ that will automate translation of biological information in a form of influence tables into logic functions. These functions can then be simulated using scenarios relevant for biological systems, such as stimulation of different cell receptors, addition of molecule inhibitors, or gene knockouts. The methods and techniques that will be used in this project include existing circuit design automation tools and algorithms, such as Espresso and logic minimization. These methods will be modified as needed to fit specifics of biological networks. Finally, this project will also include a comparison of different approaches for simulating these biological network models (synchronous, asynchronous and combined scheme), as well as comparison of simulation runtimes on CPUs and GPUs.

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