Undergrad Research Project - Automation of Model Development for Studying Big Mechanisms in Biology

Fall 2015

Student
Kyuin Lee
Advisor
Natasa Miskov-Zivanov
Project description

Developing accurate models of cell signaling networks is critical for making predictions about cell responses to stimulations such as pathogens or drugs. Such models can be built at different levels of abstractions, depending on the current knowledge about the studied system. The goal of this project is to contribute to automation of extracting information from vast amount of literature and adding this information to models of mechanisms in cell, as well as on developing accurate and efficient model simulator. In order to add extracted information to the model, we need to first define common representation language for model and new information, and define rules for adding different types of information to the model. In this project we will first focus on efficient translation of model into this common representation. Next, we will work in improving the model simulator. I will specifically implement algorithm for probability computation and modify model files to add these probabilities to the model in C language.

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