Project Mentor

Dr. Michael Blinov
Center for Cell Analysis and Modeling

Undergraduate Research Opportunity Description

Project Description	Our Center is developing software for modeling and simulation of biological models. We maintain Virtual Cell (http://vcell.org) – a general web-based framework (written in Java), and interested in providing interfacing with other tools. The student is expected to modify code of SloppyCell (Python/C, http://sloppycell.sourceforge.net/) to provide seamless integration of I/O structure with VCell. Students proficient in Perl can do the same for BioNetFit (http://bionetfit.nau.edu), while C++ developers can work with NFSim (http://nfsim.org).
Project Direction	The world of tools for Systems Biology is very broad. We are interested to develop Cytoscape plugins (Java, http://www.cytoscape.org/), integrate PySB (Python, http://pysb.org/). Development of core VCell features is an ultimate job that is on the interface of science and programming, and may lead to a future full-time employment.
Mentorship and Supervision	The project provides a lot of opportunities to improve programming skills, learn new modeling and simulation techniques, as well as develop familiarity with current research that uses these methods and tools. Beside direct supervision on the project, a student will have an opportunity to communicate with scientists that use the tools under development. We encourage attending research in progress seminars that take place every Friday at noon (including summer time) and have free soda and pizza.
Student Qualifications	Good programming experience with at least one of: Python, Perl, Java, C++. The preferred project will involve coding in Python, but there are projects for good coders in Java, Perl, C++. General familiarity with a concept of biological modeling. The interest in doing both programming and biological science.
Summer Schedule Options	Research Dates: 9-10 full-time weeks to be scheduled between May 8 and August 25, 2017 Schedule: Flexible. We provide powerful desktop computers with large screens and comfortable chairs. Although being physically in the lab is essential for the successful start of the project, a lot of coding later on can be done remotely with all issues being resolved via videoconferencing/screen sharing.
Project Continuation	Fall 2017, Spring 2018
Academic Year Time Commitment	6-9 hours/week
Possible Thesis Project	Yes

Application

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, and a brief statement of career interests.