BISC 479–Computational Physiology - Fall 2014
225Shoemaker (Lecture 11:00am – 12:50 pm, T)
Instructor:
Dr. Carol A. BritsonOffice: 206 Shoemaker
Phone: 915-7988Email:
Office Hours: Wednesdays and Thursdays 10-11:30am, or by appointment
Lecture Text (required):
You will need to have access to an advanced, undergraduate level physiology textbook. Titles authored by Sherwood, Silverthorn, Widmaier, or Fox are acceptable as is the open source text from WikiBooks.
Sherwood, L. 2012. Human Physiology: From Cells to Systems. 8th Edition. ISBN: 9781111577438.
Brooks/Cole Publishing, Pacific Grove, CA.
Silverthorn, D.U. 2013. Human Physiology: An Integrated Approach. 6th Edition. ISBN: 978-0-321-75007-5.
Pearson Education, Inc.
Widmaier, E.P., H. Raff, and K. T. Strang. 2013.Vander’s Human Physiology: The Mechanisms of Body
Function. 13th Edition. ISBN: 978-0073378305.McGraw-Hill, Inc.
Fox, S. I. 2012. Human Physiology. 13th Edition. ISBN: 978-0073403625.McGraw-Hill, Inc.
Open Source Test:
Additional texts, journal articles, and simulation/modelling software will be available in class or on BlackBoard.
BlackBoard: All students at the University of Mississippi have a WebID (and associated password) that is used to access
online resources (e.g., registering for classes, etc.) and the university’s course management system. You are already enrolled as a BlackBoard user for this course (and perhaps several other courses as well). I will be posting announcements, web links, and other information on BlackBoard. Please note that many of the files contain copywrited information from the publishers. They are for your use only as a student in this course. Attempts to distribute the files for financial gain is a violation of copywrite laws and the university's IT appropriate use policy.
Course Description & Objectives:
In this integrative course students will apply mathematical techniques and computer modelling to the understanding of physiological function. The fundamental equations and models used to demonstrate effects of functional processes (e.g., diffusion, clearance, physiological dead space, output, etc.) in the living organism will be explored through exploration of mathematical issues, models of physiological systems, modelling applications, clinical cases, and experimental design.
Objectives for this course incorporate National Science Foundation Vision and Change Core Concepts and Competencies as well as American Association of Medical Colleges Pre-Health Competencies. Specifically, by the end of the course students will develop proficiency in:
-Demonstrated understanding of the relationship between structure and function in living organisms.
-Integration of physical laws, chemical principles, and mathematical concepts on homeostasis and energy transfer in living organisms.
-Use of quantitative reasoning and models or simulations to study living organisms.
-Interpreting experimental data, forming conclusions based on data, and designing potential experiments based on the students’ conclusions.
Our primary study subject will be the human body, though examples will be presented from other organisms to examine the variety in physiological mechanisms.
Course Policies:
Attendance: You are expected to attend all lectures and you will be held responsible for all announcements.
Students who are absent on the first day of class will be dropped from the class by the Dean of the College of Liberal Arts.
Grading:You will be evaluated on your performance in both the lecture and laboratory portions of this course. Your final
grade will be determined by the scale shown below. There will be NO extra credit points.All students will be treated equally and fairly, and all grades will be calculated in the same way, regardless of extenuating circumstances or any other reason(s) not related to your actual performance in the course. Biology majors and minors need to earn a grade of C or better in this course to fulfill degree requirements.The grade of C- will not be used in the course. For additional information on the plus/minus grading system, please visit
Grade / Percent ScoreA / 93-100
A- / 90-92.99
B+ / 87-89.99
B / 83-86.99
B- / 80-82.99
C+ / 75-79.99
C / 70-74.99
D / 60-69.99%
F / 0-59.99%
The distribution of graded material is shown below:
Category / Item / % of gradeClassic paper analyses / 25
Simulation data interpretation reports / 25
Computational case studies / 25
Exams / 25
Total / 100
Make-up Course Work: Make-up course work will be allowed at the discretion of the instructor under the following
circumstances: major illness with physician documentation, family emergency with documentation and contact person, or a University-sponsored function with written documentation from the sponsoring department. Advance notification for a missed exam is essential except under extreme circumstances, in which case the instructor MUST be notified by 5pm the day of the exam. During the examination period, exams will NOT be passed out to student(s) UNDER ANY CIRCUMSTANCES after 20 minutes have elapsed from the start of the exam (i.e., DON'T OVERSLEEP!).
Student conduct:
(1) Academic dishonesty of any kind will NOT be tolerated. If caught cheating or plagiarizing, you will be reported to the university's Academic Discipline Committee for disciplinary actions.
(2) Laptop or tablet computers are allowed for note-taking purposes ONLY. Any student found using a laptop or tablet to ‘surf the web’, check social networking sites, watch a movie, or shop will be asked to leave.
(3) All other electronic devices (including, but not limited to iPods; smartphones; etc.) must be SILENCED during class. Texting is explicitly prohibited. There will be no exceptions, and violators will be asked to leave.
(3) Use correct grammar in written correspondence (including email), and refrain from using “texting” lingo.
(4) Do not enter faculty offices without knocking.
(5) Email is the best way to contact me. Emails will be returned within 24 hours during normal working hours (e.g., approximately 8am-5pm Monday – Friday).
Inclement Weather: In the event that the University cancels classes due to inclement weather, we will adjust the schedule
accordingly. For lecture we will shift our topic or event (e.g., exam) to the next class period. For laboratory, students will schedule open lab periods.
Course Schedule:Topics, resources, and assessment dates are on the following page. Any changes to this schedule will be announced in class.
Computational Physiology Fall 2014
Week of: / Topic / AssessmentsAugust 25 /
Introduction, survey of resources
September 2 /Respiration: gas volumes and environmental variables
/ Classic paper analysis,simulation report
September 8 / Respiration: dissolved gases, surface tension, and alveolar function / Classic paper analysis,
computational case study
September 15 / Respiration: lung volumes, body status, and conditioning / Classic paper analysis,
simulation report
September 22 / Body Fluids: electroneutrality, the Goldman equation, mineral regulation / Classic paper analysis,
computational case study
September 29 / Exam
October 6 / Cardiovascular function: cardiac output / Classic paper analysis,
simulation report
October 13 / Cardiovascular function: resistance, fluid dynamics / Classic paper analysis,
computational case study
October 20 / Cardiovascular function: bulk flow and ultrafiltration / Classic paper analysis,
simulation report
October 27 / Acid-Base Balance: CO2-HCO3- equilibrium (Henderson-Hasselbalch equation) / Classic paper analysis,
computational case study
November 3 / Exam
November 10 / Energy & Metabolism: BMR, energy costs of being a student / Classic paper analysis,
simulation report
November 17 / Renal Function: glomerular filtration rate, renal plasma flow / Classic paper analysis,
computational case study
November 24 /
Thanksgiving Break
December 1 /Renal Function: flow, volume, and composition of urine; allometry of renal mitochondrial function
/ Classic paper analysis, simulation reportDecember 8 /