Biological Systems Simulation
Semester Taught - Fall
Introduction to concepts and methods of process-based modeling of biological systems; physiological, populational, and agricultural applications.
MAC 2312. This course assumes no modeling experience or computer programming. Familiarity with differential equations can aid in most sections of the course.
This course serves as an introductory graduate class for modeling biological processes and systems at a variety of scales with a special emphasis on the integration of systems description, model designs and computer code implementation.
It is expected that students will have access to their own computer for this course. A laptop computer is strongly recommended for all laboratory periods so that students can use the same computer for labs as they will use in homework assignments.
At least different three computer programming languages will be used in this course; Basic, R and Java. Other languages may be used with the permission of the instructor. In addition, several freely available will be used in this class (Nova, Netlogo and QnD). Often homework assignments may include two or more languages to be used in creating solutions. This multi-platform perspective is useful in helping to determine the relative strengths and weaknesses of each language. The freeware compilers and platforms will be used to compile and execute these languages on students’ own computers. While some class time will be devoted to programming design, syntax and debugging, it is expected that the student will spend additional time outside of class to learn the basic rudiments, syntax and logic of these languages. Additional tutorial links will be provided in Sakai.
The course covers a core curriculum of system description techniques such as traditional systems dynamics (Forrester) as well as more recent interdisciplinary approaches such as Soft Systems Analysis (Checkland). Systems description in words and mathematical equations
are then translated into model designs through flow charts, pseudo-code, free-form languages
(XML,NetLogo script or Nova script) or Unified Modeling Language (UML). Subsequently, these model designs are translated into computer code (in our case, BASIC, FORTRAN, R,
Java or any student-selected code language) for simulation on computer platforms.
This description-to-design-to-code methodology will be emphasized throughout the semester on various semester assignments. Individual assignments can be strictly biological in nature or can combine biological, ecological, sociological and/or economic processes.
Dr. Greg Kiker
352-392-1864 ext. 291
Dr. Rafael Muñoz-Carpena
352-392-1864 ext. 287
Dr. Ray Huffaker
352-392-1864 ext. 281
Class Materials Required
Recommended (not required) Course Texts:
- Keen, R.E. and Spain, J.D. 1992. Computer Simulation in Biology: a BASIC
introduction. Wiley-Liss. ISBN: 0-471-50971-X. (Out of Print)
- Selected journal articles and web links will provided in Sakai
Required software (all open-source and freely available):
- Procedural languages
- BASIC compiler - http://justbasic.com
- Object-oriented design and programming
- Free form environmental models
Additional/Outside Readings (helpful but not assigned):
- Bolker, B. 2008. Ecological Models and Data in R. Princeton University Press.
- Grimm,V. and Railsback, S. 2005. Agent-based and Individual-based Modeling: A Practical Introduction. Princeton University Press.
- Software Engineering Techniques Applied to Agricultural Systems: An Object- Oriented and UML Approach by Papajorgji, Petraq J. / Pardalos, Panos M. ISBN: 0387281703, Publisher: Springer-Verlag. Published September 2005; Hardcover; 247 pages. (Available in the UF Library as an E-Book)
- Roff, D. 2010. Modeling Evolution: an introduction to numerical methods. Oxford University Press. ISBN 978-0-19-957114-7.
- Forrester, J.W. 1961. Industrial Dynamics. John Wiley. New York.
- Checkland, Peter (1999). Systems Thinking, Systems Practice. London, John Wiley & Sons. ISBN 0-471-98606-2.
- Peart, R.M. and R.B. Curry. 1998. Agricultural Systems Modeling and Simulation. Marcel Dekker, Inc. New York. 696 pp. ISBN: 9780824700416.
Additional reading materials, videos, tutorials, course notes, lectures, web sites and diagrams are also provided online through E-Learning.
At the close of this course, the student will be able to:
- Conceptualize, design and implement a variety of simple and intermediate biological system models
- Translate complex biological systems into simplified concepts/descriptions
- Translate simplified concepts/descriptions into equations and model designs
- Translate equations and model designs into computer source code
- Utilize Integrated Development Environments to implement and debug computer
code in two or more functional programming languages and/or free-form scripts
- Test and parameterize models against measured data to build confidence in simulations
Course Format: Lectures are given on two days (Tuesday and Thursday) with a Wednesday laboratory for additional lectures, discussions, computer work or to initiate homework assignments. All topics are delivered through the Sakai software and will be introduced in the class.
- Week 1: Class Introduction, Scopes of Work, Complex System Descriptions and Design (Checkland)
- Week 2: Simple System Descriptions and Design (Forrester)
- Week 3: Introduction to Programming and Integrated Development Environments in (BASIC, R, Java, NetLogo and Nova)
- Week 4: Numerical integration
- Keen & Spain Chapter 5
- Weeks 5, 6 and 7: Basic modeling concepts and algorithms
- Keen & Spain: Introduction section, Chapters 1 and 2
- Weeks 8, 9, 10 Growth and Movement Models of Populations and Individuals
- Keen & Spain: Chapters 8, 9, and 16
- Object-Oriented Model Design with Unified Modeling Language
- Nova, NetLogo and Java
- Weeks 11,12 and 13 Compartmental BioGeoChemical Models
- Keen & Spain: Chapters 13 and 15 Object
- Oriented Model Design with Unified Modeling Language
- QnD: pattern-based models
- Weeks 14,15 and 16: Parameterization, Model Testing & Sensitivity Analysis
- Keen & Spain: Chapters 3 and 2
This course is primarily graded on a series of assignments to create an overall term project/portfolio. Each student will submit individual written reports, designs and/or presentations that will be graded by the instructor. While actual grading time may vary, I will strive to grade your submissions within one week of receiving it.
- HW 1 : Scopes of Work/Proposals
- HW 2: Complex/Soft Systems Analysis
- HW 3: Forrester Diagrams and Systems Analysis
- HW 4: Elementary Programming Concepts with IDE’s/Numerical integration
- HW 5: Growth Models of Populations and Individuals - Initial Concepts
- HW 6: Growth Models of Populations and Individuals – Intermediate Concepts
- HW 7: Compartmental BioGeoChemical Models
- HW 8: Spatial and Agent Based Modeling
- HW 9: Parameterization, Model Testing & Sensitivity Analysis
- HW10: Monte Carlo Style Modeling
Assignments and Surveys: This course will utilize the E-Learning (Sakai) system for the submission of all homework assignments
On-Line Discussion Lists: Occasionally, we will use the on-line discussion feature of E- Learning (Sakai) system to allow for on-line discussions to share ideas and/or references.
- Class Assignments: 100%
- Homework will be assigned and will be due up to 7 - 14 days later.
- Peer grading (if assigned) will be due from 2 to 7 days later.
- Late homework will be accepted at a cost of 10% per day late (Up to a maximum of
CELL PHONES AND LATE ARRIVALS TO CLASS Students are asked to silence cell phones in class and to arrive promptly.
In 1995 the UF student body enacted an honor code and voluntarily committed itself to the highest standards of honesty and integrity. When students enroll at the university, they commit themselves to the standard drafted and enacted by students.
The Honor 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.
On all work submitted for credit by students at the university, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment."
Students should report any condition that facilitates dishonesty to the instructor, department chair, college dean, Student Honor Council, or Student Conduct and Conflict Resolution in the Dean of Students Office.
(Source: 2012-2013 Undergraduate Catalog)
It is assumed all work will be completed independently unless the assignment is defined as a group project, in writing by the instructor.
This policy will be vigorously upheld at all times in this course.
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/
All faculty, staff and students 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.
UF Counseling and Career Services
Resources are available on-campus for students having personal problems or lacking clear career and academic goals which interfere with their academic performance. These resources include:
- University Counseling and Wellness Center, 3190 Radio Road, Gainesville, FL 32611
- Career Connections Center, Reitz Union, 392-1601, career development assistance and counseling.