BIOSCI 220 : Quantitative Biology
2022 Semester Two (1225) (15 POINTS)
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 6:||Social and Environmental Responsibilities|
- Explain how models are used across the biological sciences to allow inference in the face of variability and uncertainty; to predict outcomes given starting assumptions; and to test hypotheses about biological processes. (Capability 1 and 2)
- Communicate statistical concepts and experimental outcomes clearly using language appropriate for both a scientific and non-scientific audience. (Capability 4 and 6)
- Create and communicate informative data visualisations using the R programming language. (Capability 3 and 4)
- Design an effective experiment adhering to the three fundamental principles: randomisation, replication, and blocking. (Capability 1 and 3)
- Perform, interpret, and critique statistical regression using the R programming language. (Capability 1 and 2)
- Analyse and interpret multivariate data using an appropriate method. (Capability 1 and 2)
- Explain how a mathematical model can be used to represent a simplified biological system. (Capability 1, 2 and 4)
- Communicate the utility of mathematical representation of a complex biological process to a scientific and non-scientific audience. (Capability 3 and 4)
- Critically evaluate the assumptions of models, and how models are deployed in science and public policy. (Capability 2 and 6)
|Laboratories||40%||Group & Individual Coursework|
|Final Exam||25%||Individual Examination|
|Assessment Type||Learning Outcome Addressed|
Students must pass the practical (laboratories) and the theory (quizzes, test and exam) independently to pass the course overall.
- Introduction to R and RStudio.
- Data exploration and visualization.
- Experimental design.
- Hypothesis testing and interpretation of p-values.
- Linear regression models; model critique and comparison.
- Multivariate data analysis, introduction to dimensionality reduction.
- What is (forward) modelling and why we do it.
- Mathematical reasoning and vocabulary.
- Introduction to growth (and death) models.
- Logistic model for resource-limited growth.
- SIR model (Susceptible-Infectious-Recovered) for the spread of infectious disease.
- Assumptions made by models and when and why these may be justified.
- Model-based inference, parameter inference with Maximum Likelihood, fitting curvilinear models.
- Statistical model comparison, using the principle of parsimony to penalise more complex models (with AIC). Fitting SIR models to real-world SARS-CoV-2 data.
- The crucial role of models in science & society; critical thinking about models, inference, and public policy.
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.
For this course, you can expect 2 hours of lectures, a three hour laboratory (one week off, two weeks on), 3 hours of reading and thinking about the content and 3 hours of work on assignments and/or test preparation.
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.
Otherwise, this course is designated a "campus experience," meaning:
- Attendance is expected at scheduled activities including labs to complete components of the course.
- Lectures will be available as recordings. Other learning activities including labs/studios will not be available as recordings, unless the entire campus is forced online due an increase in the COVID-19 Alert Level (see Learning Continuity section for more details).
- The course will not include live online events, unless the entire campus is forced online due an increase in the COVID-19 Alert Level (see Learning Continuity section for more details).
- Attendance on campus is required for the test & exam (except for remote/otherwise exempt students).
- The activities for the course are scheduled as a standard weekly timetable.
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.
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.
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.
Class representatives are students tasked with representing student issues to departments, faculties, and the wider university. If you have a complaint about this course, please contact your class rep who will know how to raise it in the right channels. See your departmental noticeboard for contact details for your class reps.
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.
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 http://disability.auckland.ac.nz
Your course coordinator is Jenn Jury (email email@example.com). Please let me know how best we can support you in this course.
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 https://www.auckland.ac.nz/en/students/academic-information/exams-and-final-results/during-exams/aegrotat-and-compassionate-consideration.html.
This should be done as soon as possible and no later than seven days after the affected test or exam date.
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 course assessment continues to meet the principles of the University’s assessment policy. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator/director, and if disruption occurs you should refer to the university website for information about how to proceed.
The delivery mode may change depending on COVID restrictions. Any changes will be communicated through Canvas.
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 https://www.auckland.ac.nz/en/students/forms-policies-and-guidelines/student-policies-and-guidelines/student-charter.html.
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 students may be asked to submit 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. In exceptional circumstances changes to elements of this course may be necessary at short notice. Students enrolled in this course will be informed of any such changes and the reasons for them, as soon as possible, through Canvas.