University of Florida

ABE 4662
Quantification of Biological Processes

Semester Taught - Fall

Catalog Description

Credits: 3

Quantitative description and analysis of biological processes pertaining to microbes, plants, animals, and ecosystems. Biological transport phenomena, bioenergetics, enzyme kinetics, metabolism, bioregulation, circulatory and muscle systems, and agroecosystems. Analytical and experimental laboratory for development of quantitative skills.

Pre-requisites/Co-requisites

ABE2062 or BSC2010/2011, EML3100, EGN3353 OR CWR3201, ABE3612C or EML4140

Course Objectives

  • Gain fundamental knowledge to understand quantitative descriptions and the analyses of biological processes.
  • Demonstrate proficiency in the use of computational tools to analyze and model biological processes.
  • Identify, formulate, and solve problems related to biological processes.
  • Develop teamwork and presentation skills to report and solve problems related to biological processes.

Contributions of Course to Meeting the Professional Component for ABET

This course contributes 3 credit hours toward meeting the minimum 48 credit hours of Engineering Topics in the basic-level curriculum for the Bachelor of Science Degree in Agricultural and Biological Engineering.

Relationship of Course to Program Outcomes

From the list of (a) through (k) program outcomes listed below, this course addresses a, b, c, e, g, and k.  

ABET Program Outcomes

  • (a) Apply knowledge of mathematics, science, and engineering
  • (b) Design and conduct experiments, as well as analyze and interpret data
  • (c) Design a system, component, or process to meet desired needs
  • (d) Function on multi-disciplinary teams
  • (e) Identify, formulate, and solve engineering problems
  • (f) Understand professional and ethical responsibilities
  • (g) Communicate effectively
  • (h) Understand the impact of engineering solutions in a global and societal context
  • (i) Recognize the need for, and engage in life long learning
  • (j) Understand contemporary engineering issues
  • (k) Use the techniques, skills, and modern engineering tools necessary for engineering practice

Instructor

Dr. Melanie Correll
Office location: 209 Rogers Hall
Telephone: 352-392-1864 x 209
E-mail: correllm@ufl.edu

 Material/Supply Fees

None

Class Materials Required

Textbook Required

  • Title: Introduction to Computational Science
    Author:  Angela B. Shiftlet and George W. Shiftlet
    Publication Date and edition:  Princeton University Press, Copyright 2006
    ISBN  Number: 0-691-12565-1 (newer second addition (2014) is also allowed)

Recommended Reading

  • Biological Process Engineering - Author: Arthur T. Johnson, Publication date and edition: John Wiley and Sons, Inc Copyright 1999 ISBN Number: 0-471-24547-X

  • Mathematical Models in Biology (An Introduction).  Author:  Elizabeth S. Allman and John Rhodes,  Publication date and edition: Cambridge University Press, Copyright 2004 ISBN Number: 0-521-52586-1

    Computer simulation in biology (A basic introduction).  Author:  Robert E. Keen and James D. Spain.  Publication date and edition: Wiley-LISS, Copywrite 1992 ISBN Number:  0-471-50971-X (out of press used versions can be had)

  • Other assigned reading material will be provided by the instructor.

Course Outline

  • Unit 1:  Introduction to Computational Tools to Analyze or Model Biological Processes
  • Unit 2:  Constrained and Unconstrained Growth in Biological Systems
  • Unit 3:  Compartmental Models (Pharmacokinetics, drug delivery)
  • Unit 4:  Numerical Methods and Errors in Modeling Processes
  • Unit 5:  Enzyme Kinetics
  • Unit 6:  Empirical Modeling and Data Analytics for Biological
  • Unit 7:  Stochastic Models and Diffusion
  • Unit 8:  Cellular automata of Biological Systems
  • Unit 9:  Matrix Methods Age-Class Models
  • Unit 10: Student Selected Unit 

Attendance and Expectations

  • Attending and participating in class is required (some material is only provided in class).  (note: all students get one free pass to miss a day unexcused)
  • Using notes, projects, reports, and/or codes from previous offerings of this course is considered cheating.
  • Giving code or other materials provided in class to other students that missed class is considered cheating.
  • Assisting other students on troubleshooting their code (this is cheating on exams or if indicated by instructor) is helpful and Not Cheating (limit the amount of code you provide so they can learn).
  • Letting the instructor know of a known missed absence ahead of time is expected.
  • Getting materials from the instructor for excused absences is expected.
  • Using professional attitudes and meeting deadlines is expected.
  • Making an appointment (or using the office hours) for out-of-class assistance with instructor prior to the day that an assignment is due is expected.
  • Putting your best effort in this course is expected.
  • Completing the To Do Lists/Assessments in the Units with your BEST EFFORT is Expected
  • Using supplemental material to cover areas you need to get to the level required by the unit is expected.
  • Late assignments (for projects and homework, no late exams are accepted except in university excused absences) start with 10% deduction at 5 minutes after the due date/time and then this 10% deduction continues until 9:35am for the next class meeting (usually a Monday). Then at 9:36am on the next class date (usually a Monday) 20% deducted until 9:35am on the next class date (usually a Wednesday) after 9:36am on this second class date (usually a Wednesday) until the end of the third class day (usually a Friday) by end of this day (5pm) 30% will be deducted. No late homework beyond the third missed class  (usually Friday) will be accepted unless arranged with Dr. Correll.

Grading

A C- will not be a qualifying grade for critical tracking courses.  In order to graduate, students must have an overall GPA and an upper-division GPA of 2.0 or better (C or better).  Note: a C- average is equivalent to a GPA of 1.67, and therefore, it does not satisfy this graduation requirement.  For more information on grades and grading policies, please visit: https://catalog.ufl.edu/ugrad/current/regulations/info/grades.aspx

Grading Scale
A 93.5-100
A- 89.5-93.4
B+ 87.5-89.4
B 83.5-87.4
B- 79.5-83.4
C+ 77.5-79.4
C 73.5-77.4
C- 69.5-73.4
D+ 67.5-69.4
D 63.5-67.4
D- 59.5-63.4.
E <59.4
Grading Method Percentage
Homework/Labs/Exercises 40%
Exam 1 15%
Exam 2_Final Exam 15%
Projects 30%
Total 100%

No make-up exams will be given except for valid medical reasons or unless prior arrangements have been made.

Academic Honesty

As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge: “We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.”  You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit at the University of Florida, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." 
 
It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code.  Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see: http://www.dso.ufl.edu/sccr/process/student-conduct-honor-code.  

Accommodation for Students with Disabilities

The Disability Resource Center coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability related issues.

0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drc/  

Software Use

All faculty, staff and student of the University are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against University policies and rules, disciplinary action will be taken as appropriate. We, the members of the University of Florida community, pledge to uphold ourselves and our peers to the highest standards of honesty and integrity.

Campus Helping Resources

Students experiencing crises or personal problems that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling & Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having personal problems or lacking clear career or academic goals, which interfere with their academic performance.

  • University Counseling & Wellness Center, 3190 Radio Road, 352-392-1575, www.counseling.ufl.edu/cwc/

    Counseling Services
    Groups and Workshops
    Outreach and Consultation
    Self-Help Library
    Training Programs
    Community Provider Database

  • Career Resource Center, First Floor JWRU, 392-1601, www.crc.ufl.edu/