HRP SU17-18: Research Opportunity with Professor James Schaff

Project Mentor

Professor James Schaff
Center for Cell Analysis and Modeling

Undergraduate Research Opportunity Description

Project Description Our Center is developing and maintaining a distributed multi-user modeling and simulation environment for cell biology ( We are interested in developing a new capability focused on model assisted analysis of microscopy experiments. This project involves developing spatial models in VCell to mathematically model specific microscopy experiments to improve the quantitative analysis of experimental data and gain new insight into the underlying biology. The specific biological system involves translation experiments of optogenetic ligands with photoactivatable membrane receptors. This project will focus on developing methodology to couple spatial modeling and image analysis and will involve some light software development.
Project Direction This project will provide relevant motivation for the integration of our VCell modeling and simulation framework with the FIJI tool for image processing of microscopy data. Previous related efforts in our group has focused on very specific experimental systems and were inflexible. This project focuses on a specific biological system at the interface between theory and experiment. This project can easily expand in scope with respect to biological complexity, experimental protocols, mathematical analysis, and software automation.
Student Qualifications This project requires a background in biology and biochemistry and an intermediate proficiency in programming (data structures, algorithms). The student should have an interest in physics, mathematics and simulation.
Summer Schedule Options Research Dates: 9-10 full-time weeks to be scheduled between June 12 and August 25, 2017
Schedule: M-F, 9am-4pm
Project Continuation Fall 2017, Spring 2018
Academic Year Time Commitment 6 hours/week
Possible Thesis Project Yes


Submit an online application for this research opportunity using the form below. The application deadline is Friday, February 24, 2017.

This application requires a cover letter, a resume or CV, an unofficial transcript, a brief statement of research interests, a brief statement of career interests, and contact information for at least one reference (a faculty member or employer who is familiar with your academic or software development qualifications).