HRP SU17-14: Research Opportunity with Dr. Pedro Mendes

Project Mentor

Dr. Pedro Mendes
Center for Quantitative Medicine

Undergraduate Research Opportunity Description

Project Description Selection of software architecture for creating multi-scale models of iron biochemistry. In our research group we have available models of iron biochemistry at different levels of representation: a) whole body and b) specific cell types. We now wish to combine these into a multi-scale model that includes both scales. There are already existing software applications that can do this in principle and we are interested in testing how these applications work.
Mentorship and Supervision The student will be trained, in the first week, the basics of computational models of biochemical networks and use of the software COPASI for their simulation. The student would then have a period of two weeks to familiarize with our two models of iron (a whole-body physiological model and a hepatocyte cellular model). Then the student would use the remainder of the time to research how to combine these two models into a single multi-scale model using two applications, FLAME and EPISIM. Training will be carried out by myself and my postdoctoral fellow (Dr. Jignesh Parmar). To monitor the student’s progress we will have weekly meetings where the student will make a presentation of the week’s progress; I will provide direct feedback to the student at those meetings.
Student Qualifications
  • – Programming/computer science skills; interest in computational biology
  • – Suitable for either a) computer science student with interest in biological applications, or b) biology/biochemistry student interested in computational biology.
Summer Schedule Options Research Dates: 9-10 full-time weeks to be scheduled between May 22 and August 4, 2017
Schedule: M-F, 9am-4pm
NOTE: This is a standalone summer opportunity that will not continue into the academic year.


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, an unofficial transcript, and a brief statement of research interests.