Project Mentor

Dr. Pedro Mendes
Department of Center for Cell Analysis and Modeling

Undergraduate Research Opportunity Description

Project Description	The project consists of an assessment of two different methods for modeling multicellular biological systems: full differential equation models and hybrid agent-based / differential equation models. A couple of representative models of multicellular systems (e.g. microbial communities, epithelial tissues, or connected spiking neurons) will be chosen from the literature, and models will be set up in the software COPASI for the full differential equations approach, and also in a combination of COPASI and Vivarium for the hybrid agent-based/differential equations approach. An assessment of the error introduced by the hybrid approach will be estimated by comparison with the full differential equation approach.
Project Direction	The project is part of a quantitative comparison of these two modeling approaches, which are currently carried out in the literature but which have never been compared . The software COPASI is created in my research group, under long-standing NIH funding, and is widely used by the research community (yearly more than 100 publications use it); thus there will be technical support to help the student. The software Vivarium is created in the research group of Dr. Agmon, a faculty member here at the Center for Cell Analysis and Modeling, and who collaborates with my research group. This project is expected to contribute to a planned peer-reviewed publication of which the student would be a co-author.
Mentorship and Supervision	I will have daily meetings with the research assistant to mentor and help keep the research on track . Weekly oral presentations by the student to the research group will provide the means to monitor progress and provide formal feedback (in addition to the daily meetings).
Student Qualifications	Students need know how to program, preferably in Python, though the project does *not* require strong programming expertise. The project would be adequate for: 1) students with a background in biology and an interest in computational modeling, or 2) students with a background in computer science, physics or mathematics, with an interest in biological applications.
Summer Schedule Options	Research Dates: May 19 to July 25, 2025 Schedule: Monday-Friday 9am through 5pm. Schedule could be made flexible as long as same amount of time is kept.
Project Continuation	Fall 2025, Spring 2026
Academic Year Time Commitment	3 6 9 hours/week
Possible Thesis Project	Yes

Application

Submit an online application for this research opportunity at https://quest.uconn.edu/prog/HRPSU25-20. The application deadline is Monday, February 17, 2025.

This application requires a resume or CV, an unofficial transcript, and a brief statement of research interests.