{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

hw2 - Computational Methods in Biology(Spring 2011...

Info icon This preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Computational Methods in Biology (Spring 2011) Assignment 2 (due in class on Feb. 18) The Rules This assignment and most of the others in this course will involve computer simu- lations. What do I expect you to turn in? I'd like the following: (1) Hand-written or word-processed text describing what you are doing, how you did it, and the results you got. I ask many questions, and I expect you to answer these. When I grade I will be looking to see if each question has been satisfactorally an- swered. Use complete sentences and make your work easy to follow. (2) Labelled gures. Include things such as gure number, axis labels, bifurcations, types of branches (stationary or periodic), nullclines ( x-nullcline or y-nullcline), and equilibrium points (what type?). In some cases I will ask for a hand-drawn gure, and this is what you should turn in. In other cases I will ask for a computer-drawn gure (the XMGR graphing package is what I use to make gures, I'll show you how to use it if you ask). In other cases I won't specify. (3) Make it look good. Wading through disorganized and unclear work does not put me in a good mood. Ask yourself whether you would want to grade it! (4) Turn it in on time. You can, however, turn it in up to two days late with a 20% reduction in grade. After that I won't accept it. 1 2 The free software package XPPAUT , written by Bard Ermentrout at the University of Pittsburgh, is a great tool for analyzing continuous dynamical systems. In this rst problem I will talk you through many of the things you need to know to use this package (on the SUNs) to do phase plane and bifurcation analysis. [Versions of this software are written for unix, linux, and even Windows machines. You can download it from Bard's web page.] The example problem will be a model of oscillatory glycolysis developed in 1972, called the Goldbeter-Lefever model . This descibes in a very simple way how the molecule ATP is converted to ADP by the enzyme phosphofructokinase. This enzy- matic function is described by \¨". The ATP input rate to the system is ν and the ADP degradation rate is η . Parameter τ is a time constant. 1. [10 points] The Goldbeter-Lefever model ( Biophysical Journal , vol. 12, pp. 1302{ 1315, 1972) is dATP dt = [ ν- ¨( ATP,ADP )] /τ dADP dt = [¨( ATP,ADP )- ηADP ] /τ . where ¨( ATP,ADP ) = ATP (1 + k ADP ) 2 , and ν , η , k , and τ are parameters. We will use k = 20 and τ = 500 throughout the assignment, and various values for ν and η . (a) The computer code for the Goldbeter-Lefever model, goldbeter.ode , can be downloaded from my website (www.math.fsu.edu/ ∼ bertram/course software). If you look in this le you will see how easy it is to enter ODEs and associated information into this program. On the SUNs start up xpp using the command \xppaut gold- beter.ode". Notice the buttons on the top of the xpp screen. Clicking on these will open other windows that will allow you to do things like change the values of the system parameters.system parameters....
View Full Document

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern