HRP SU23-4: Research Opportunity with Dr. Michael Blinov

Project Mentor

Dr. Michael Blinov
Center for Cell Analysis and Modeling, Department of Genetics and Genome Sciences

Undergraduate Research Opportunity Description

Project Description Mathematical modeling of biological processes is important to gain an understanding of the underlying biological mechanisms and predict the 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 ( software using GUI. We will develop an infrastructure and a set of small models (ModelBricks, that serve as building blocks for larger models.
Project Direction The ModelBricks project ( is ongoing and can accommodate students with an 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.
Check my webpage at and feel free to email me with any questions.
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 students participate in; it serves as a jump-start for the project. Progress will be measured in the amount of code written/text extracted/cartoons drawn/models designed – very visual and easy to track. I need all the results immediately, so the work will be highly interactive.
Student Qualifications I’m doing purely computational research. Coding is preferable (JavaScript, Python, HTML/CSS, Ruby, PROLOG). Alternatively, I can offer projects in modeling with GUI tools (, web development (GitHub pages), and visualization (using graphical tools from Students will learn a lot about computational project management (e.g., master GitHub). The basics of chemical kinetics (species, reactions, mass-action) is a plus. Interested in biology students are invited as well: they will read papers and assist in model creation by systematizing and entering data through the web interface.
Summer Schedule Options Research Dates: May 22 to July 28, 2023
Schedule: Flexible. Usually, I expect students to start 6-8 hours a day working in my lab for the first week. As the project is computer-based, the schedule becomes more flexible with the possibility to work from home during the next weeks. Note: The Health Research Program has certain in-person participation requirements, including a presentation at Summer Research Day, that a student working in a hybrid arrangement would be expected to satisfy.
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, a brief statement of research interests, and a brief statement of career interests. For coding students, links to projects, GitHub handle, etc. would be useful – please include in application materials. References should be available upon request.