Math 593B/793F Fall 2014

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Course Information[edit]

Description: Mathematical Systems Biology.

Instructor: Casian Pantea. email me

Class schedule: Tuesdays, Thursdays, 8:30-9:45AM in Armstrong 313

Office hours: Tuesdays 5-6PM, Thursdays 2-3PM, and by appointment, in Armstrong Hall 305B

Info sheet containing more or less the stuff on this webpage.

Textbooks and resources[edit]


Sontag, Lecture Notes on Mathematical Systems Biology

Useful free resources:

Linear algebra notes

Linear Algebra Done Wrong, Treil
Linear Algebra -- wiki textbook

Web goodies

Khan Academy


Grading scheme[edit]

  • 30% Final exam on Tuesday December 11 2014, 11AM-1PM in Armstrong 315
  • 25% Midterm exam
  • 45% Homework assignments
  • (793F only) 20% Project (homework, midterm and final are rescaled to sum up to 80%)


  • Homework will be assigned once every three weeks, and due two weeks later (please see the course schedule below for exact dates).
  • Late turn-ins will not be accepted.


  • There will be one in-class midterm exam, on October 21.
  • No make-up midterm will be given.

Final Exam[edit]

  • Tuesday December 11 2014, 11AM-1PM in Armstrong 315.
  • Final is cumulative.

Course Schedule (subject to changes)[edit]

Date Topic Resources HW/Exams
Aug 19 Introduction; exponential growth, logistic growth 1.1
Aug 21 Chemostat; Michaelis-Menten 1.1
Aug 26 Steady states; linear stability analysis 1.2
Aug 28 Vector fields; phase planes 1.4
Sep 2 Nullclines; local and global stability 1.4
Sep 4 SIRS model 1.5 HW 1 posted
Sep 9 Chemical kinetics 1.6
Sep 11 Interaction graph; Matlab interlude 1.5
Sep 16 Enzyme kinetics. QSSA 1.6
Sep 18 Inhibition 1.6 HW 1 due
Sep 23 Gene expression. Cooperativity 1.6
Sep 25 Deficiency theory
Sep 30 Hill kinetics. Ultrasensitivity 1.7
Oct 2 Goldbeter-Koshland model and ultrasensitivity. Bistability 1.7
Oct 7 Limit cycles 1.8 HW 2 posted
Oct 9 Bifurcations 1.9
Oct 16 Review 1.9
Oct 21 Midterm 1 Midterm solutions
Oct 23 Chapter 1 Review 1.9
Oct 28 Hopf bifurcations 1.9
Oct 30 Matlab. XPP HW 2 due
Nov 6 Oscillating chemical networks
Nov 13 Graphical conditions for multistationarity: the DSR graph
Nov 18 Research project: dynamics of 2D chemical networks
Nov 20 Introduction to PDE models 2.1 HW 3 posted
Dec 2 Transport 2.1
Dec 4 Chemotaxis 2.1
Dec 9 Diffusion 2.2
Dec 11 Final exam Solutions to final

Inclusivity statement[edit]

The West Virginia University community is committed to creating and fostering a positive learning and working environment based on open communication, mutual respect, and inclusion. If you are a person with a disability and anticipate needing any type of accommodation in order to participate in this class, please advise me and make appropriate arrangements with the Office of Accessibility Services (293-6700). For more information on West Virginia University's Diversity, Equity, and Inclusion initiatives, please see