SKILL SHEET

BIOLOGICAL MODELING UNIT

COMPUTATIONAL BIOLOGY COURSES 03-310, 03-510 AND 03-710

This is an organized listing of skills and concepts designed to help you prepare for exams. This list is aimed at focusing your attention on those parts of the course material related to skills you may be required to perform. This is NOT an exhaustive list of concepts - not all material from the lectures is listed here, so you should still review your course notes and assigned reading. SKILLS AND CONCEPTS WHICH ARE NOT LISTED HERE MAY BE INCLUDED ON EXAMS. Unless noted below, all material is relevant to all courses (but the depth of understanding is expected to be greater for 03-510/ 03-710).

• Ionization equilibira for amino acids
• Absolute reference and relative reference in spreadsheets
• forward references & recalculation order
• circular references
• convergent vs. divergent
• testing for convergence (stability)
• Goal seek
• recursion relations
• steady state values
• parameter lines/planes
• transition values
• biochemical kinetics
• difference equations
• differential equations: solve analytically vs. numerical
• 3 things needed to solve differential equations
• differential equations
• parameter values
• boundary conditions
• timescale & integration interval (step size)
• numerical integration of diff. eq. with Excel
• accuracy of Euler's method (f' increasing -> underestimates)
• midpoint method and fourth-order Runge-Kutta method
• solving single differential with Maple (analytical)
• specifying symbolic boundary conditions
• solving set of diff. eq. numerically with Maple
• plotting with odeplot
• plotting and interpreting phase planes
• compartmental analysis
• definition of compartment
• analytical solution for first-order compartmental models with constant inputs
• numerical solution for first-order compartmental models with varyding inputs
• basic neurophysiology
• threshold voltage for action potential
• Hodgkin-Huxley model
• not mechanistic, empirical
• definitions of gate parameters
• interpretation of V vs. m and V vs. n phase planes
• cell cycle model (4 phases)
• Cyclin/Cdk vs. APC phase plane
• Bifurcation of cyclin/Cdk vs. “p” phase plane
• Kenetics of cell cycle changes in cyclin and APC
• (03-510/03-710) Virtual Cell for Cell Modeling

Prepared by Robert F. Murphy, May 8, 1997

Revised by Robert F. Murphy, May 3, 1999

Revised by Robert F. Murphy, May 2, 2002

Revised by Yanhua Hu and Shann-Chig Chen, April 25, 2005