HRP SU17-18: Research Opportunity with Dr. James Schaff

Project Mentor

Dr. 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 exposing VCell’s simulation and data analysis capabilities through a Python API communicating with our local VCell client (java) and our remote RESTful VCell API. We will use this capability to provide a IPython/Jupyter notebook for the interactive scripting of VCell for running simulations and performing data analysis with VCell.
Project Direction This project will form the basis for our integration with other simulation and analysis libraries such as those in SciPy and more specific FEniCS, PyURDME, COPASI and for custom interactive visualization using the Visualization Toolkit. The Jupyter notebook capabilities will be expanded to include the integration other libraries for parameter estimation and custom data analysis.
Student Qualifications This project requires an intermediate proficiency in programming (data structures, algorithms) and familiarity with python and Java. The student should have an interest in physics, mathematics and simulation. Some exposure to numerical methods, simulation or data analysis would be helpful.
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).