Project Mentor

Dr. Michael Blinov
Center for Cell Analysis and Modeling

Undergraduate Research Opportunity Description

Project Description	Mathematical modeling of biological processes is important to gain understanding of the underlying biological mechanisms and predict dynamics and outcomes of experiments and medical interventions. Mathematical models describe interactions among components of biological systems. Models are implemented and simulated in the Virtual Cell (http://vcell.org) software using GUI. We will develop a set of small models (ModelBricks, http://modelbricks.org) that serve as building blocks for larger models. A related project is connecting them to ImageJ software.
Project Direction	The ModelBricks project (http://modelbricks.org/) is ongoing and can accommodate students with interest in applications of computers and mathematics to biology in many directions: reading publications and understanding biological mechanisms, using software to model, coding, web development, visualization using graphical tools. A related project is connecting ModelBricks to ImageJ software.
Mentorship and Supervision	We usually organize a weekly summer students seminar, where each student is talking for 10-15 minutes about his/her progress for the week, with other students and faculty asking questions. Mid June we have a three-day Virtual Cell workshop that students participate in; it serves a a jump-start for the project. Progress will be measured in the amount of text extracted/cartoons drawn/models designed/code written – very visual and easy to track. I need all the results immediately, so the work will be highly interactive.
Student Qualifications	Desire to spend time in front of a computer and do either coding (Javascript, Python, HTML/CSS) or reading papers. Different skills can be utilized: simple use of graphical tools (http://sbgn.org), modeling with GUI tools (VCell), web development (github), coding (Python, Java, Ruby, api). Students will learn a lot about computational projects management, e.g. master github. Basics of chemical kinetics (species, reactions, mass-action) is a plus. Students interested in biology will do less coding but read papers and assist in model creation.
Summer Schedule Options	Research Dates: May 24 to July 30, 2021 Schedule: M-F, 8am-4:30pm
Project Continuation	Fall 2021, Spring 2022
Academic Year Time Commitment	3-9 hours/week
Possible Thesis Project	Yes

Application

Submit an online application for this research opportunity at https://quest.uconn.edu/prog/HRP21-4. The application deadline is Monday, February 1, 2021.

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