BIOSCI 702 : Modelling Biological Processes


2021 Semester Two (1215) (15 POINTS)

Course Prescription

Modelling and simulation are increasingly important aspects of the biological sciences. A variety of biological modelling approaches are introduced through a series of practical exercises to build and analyse models of biological processes. Topics include modelling in ecology and systems biology, agent-based modelling of complex biological systems, and molecular dynamics of biological molecules.

Course Overview

This is a hands-on modelling course for students with no prior experience in modelling. The course involves a series of practical tasks and exercises preceded by lectures with accompanying readings and discussions (1hr lecture followed by 3hr computational lab every week). The skills developed in this course are particularly useful for those wishing to have a career involving quantitative thinking and computational modelling. The course consists of three modules (please see Key Topics for more information):
  1. modelling in ecology and systems biology
  2. agent-based modelling in complex systems
  3. molecular dynamics of biological molecules
  •  The primary prerequisite is that you are interested in learning material that falls at the interface between biology and modelling.
  • For students with a background in biology: you should be willing to do high school level algebra (Module 1) and to learn to modify computer programs (Module 2 and 3). You do not need to know how to write a computer program from scratch.
  • For students with a background in computer science, physics, applied mathematics: you should have a strong interest in biology.

Course Requirements

Restriction: BIOINF 703

Capabilities Developed in this Course

Capability 1: Disciplinary Knowledge and Practice
Capability 2: Critical Thinking
Capability 3: Solution Seeking
Capability 4: Communication and Engagement
Capability 5: Independence and Integrity
Graduate Profile: Master of Science

Learning Outcomes

By the end of this course, students will be able to:
  1. Describe and explain the different types of models and how they help us to investigate and understand the natural world (Capability 1, 2 and 4)
  2. Be able to formulate scientific concepts into simple conceptual, mathematical or algebraic models and use these to test hypotheses (Capability 1, 2 and 3)
  3. Be able to modify simple computer programs to test hypotheses or adapt them to new situations (Capability 1, 2 and 3)
  4. Be able to work independently and with others to identify and answer scientific questions (Capability 1, 2, 3, 4 and 5)
  5. Be able to work independently and with others to identify and solve problems (Capability 1, 2, 3, 4 and 5)
  6. Communicate results of independent and group investigations to a broad scientific audience (Capability 1, 2, 4 and 5)
  7. Analyse and discuss literature describing the application of systems concepts and modelling across a range of natural sciences (Capability 1, 2 and 4)


Assessment Type Percentage Classification
Engagement with weekly discusion sessions 10% Individual Coursework
Use of computer software to evaluate mathematical models 30% Individual Coursework
Modification of simple computer program to investigate behaviour of microscopic systems 30% Individual Coursework
Modification of simple computer program to investigate behaviour of macroscopic systems 30% Individual Coursework
Assessment Type Learning Outcome Addressed
1 2 3 4 5 6 7
Engagement with weekly discusion sessions
Use of computer software to evaluate mathematical models
Modification of simple computer program to investigate behaviour of microscopic systems
Modification of simple computer program to investigate behaviour of macroscopic systems

Key Topics

The course consists of three modules:
  1. modelling in ecology and systems biology (Dr Nobuto Takeuchi,
  2. agent-based modelling in complex systems (Dr Matthew Egbert,
  3. molecular dynamics of biological molecules (AP Jane Allison,
Module 1 will provide an introduction to modelling in ecology and systems biology. It will teach how to model the dynamical aspects of ecological populations and molecular systems. During this module, you will have ample opportunities to interpret and analyze simple mathematical models using algebra (high school level) and computer software. After completing this module, you will be able to read and interpret modelling papers in ecology and systems biology.

Module 2 will provide an introduction to agent-based modelling in complex systems. It will teach how to model spatial pattern formation and self-organisation in complex systems. It will involve a series of computer-based exercises, during which you will have the opportunity to modify some simple computer programs for simulating complex systems.

Module 3 will provide an understanding of how the chemical and structural properties of molecules and their dynamics are represented mathematically and computationally. During this module, you will have the opportunity to modify and even write some simple code for simulating molecular dynamics, as well as use the sophisticated programs used by researchers to simulate biological molecules such as proteins.

Special Requirements


Workload Expectations

You can expect one hour of lecture and three hours of lab, three hours of reading, three hours of work on assignments per week. (This course is a standard 15 point course and students are expected to spend 10 hours per week involved in each 15 point course that they are enrolled in.)

Delivery Mode

Campus Experience

Attendance is expected at scheduled activities including labs to receive credit for components of the course. Lectures will be available as recordings. Other learning activities including labs will not be available as recordings. The course will not include live online events. Attendance on campus is not required for the test/exam. The activities for the course are scheduled as a standard weekly timetable delivery. A remote version of the course can be made available to students located overseas because of border restrictions, or those with an exemption to study remotely.

Learning Resources


Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Digital Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.

The online version of this course will be made available to approved students unable to travel to Auckland.

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed against online source material using computerised detection mechanisms.


The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Learning Continuity

In the event of an unexpected disruption we undertake to maintain the continuity and standard of teaching and learning in all your courses throughout the year. If there are unexpected disruptions the University has contingency plans to ensure that access to your course continues and your assessment is fair, and not compromised. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator, and if disruption occurs you should refer to the University Website for information about how to proceed.

Alert Level 1:  Delivered normally as specified in delivery mode
Alert Level 2: You will not be required to attend in person.  All teaching and assessment will have a remote option.  The following activities will also have an on-campus or in-person option: lectures, labs.
Alert Level 3 or 4: All teaching activities and assessments are delivered remotely

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter


Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course you may be asked to submit your coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. The final decision on the completion mode for a test or examination, and remote invigilation arrangements where applicable, will be advised to students at least 10 days prior to the scheduled date of the assessment, or in the case of an examination when the examination timetable is published.

Published on 14/12/2020 09:59 a.m.