HRP SU23-2: Research Opportunity with Dr. Eran Agmon

Project Mentor

Dr. Eran Agmon
Center for Cell Analysis and Modeling, Department of Molecular Biology and Biophysics, Department of Biomedical Engineering

Undergraduate Research Opportunity Description

Project Description For this summer project, the student will work on a computational model of bacterial interactions in the human gut microbiome. The student will write code to add new mechanistic details to the model of the microbiome, will simulate it, visualize the results, and evaluate the results by comparing with experimental data. The final model and results will be presented in a Python notebook and shared online for others to learn from.
Project Direction We are a systems biology laboratory that specializes in multi-scale modeling of microbiomes – from their molecular underpinnings, to individual cellular functions, to multi-cell interactions in an environment. Microbiomes are a powerful layer of biological complexity that have co-evolved with our bodies and interact closely with our cells, and understanding their behavior could have implications for immune health, metabolism, and synthetic biology. Building these models requires us to develop new computational methods for combining multi-source and multi-level data with diverse models of biological mechanisms.
Mentorship and Supervision We will have bi-weekly meetings to talk about the project’s progress and barriers to progress. The student will also meet other scientists involved in the project to learn about their work. The student will receive code-specific feedback through our GitHub project page, with suggestions about how to improve the code.
Student Qualifications The student must have a basic understanding of molecular and cellular biology, an interest in building complex mathematical models, and experience programming in Python.
Summer Schedule Options Research Dates: May 22 to July 28, 2023
Schedule: To be arranged within schedule parameters of M-F, 9am-6pm
Project Continuation Fall 2023, Spring 2024
Academic Year Time Commitment 3-9 hours/week
Possible Thesis Project Yes


Submit an online application for this research opportunity at The application deadline is Monday, January 30, 2023.

This application requires a cover letter, a resume or CV, an unofficial transcript, GPA, Science GPA, a brief statement of research interests, and a brief statement of career interests.