Biological research techniques are changing rapidly, and each year we learn about new ways of collecting and analysing large biological datasets. New empirical data often require novel methods of analysis, and large datasets require advanced computational techniques to handle. Quantitative biologists also frequently rely on mathematical and simulation models to explore and understand complex biological processes and patterns. At the heart of quantitative biology is asking the right question, in the right way, with traditional experimental design during data collection being replaced by (i) decisions about how to partition existing datasets and (ii) parameter definitions in simulation models to effectively answer outstanding biological questions. Students will learn about advanced methods in quantitative biology, from study design, reading and writing skills, through to theory and agent-based modelling, mining citizen-science data, analysing of animal tracking data, and using deep-learning method.

Learning Outcomes

Upon successful completion, students will have the knowledge and skills to:

1. Describe, present, and critically evaluate analytical methods, models and theories used in published research.
2. Develop skills in experimental design when using simulations or analysing existing datasets, including making appropriate assumptions and identifying the core biological measures of interest.
3. Identify appropriate approaches for posing questions and designing analyses when testing hypotheses using automated data collection method.

Research-Led Teaching

Assignments 1 & 2 will give the students first-hand experience on key processes in biological research, including developing research questions, developing data collection and analytical methods, and generating and writing results.

Recommended Resources

Recommended student system requirements 

ANU courses commonly use a number of online resources and activities including:

• video material, similar to YouTube, for lectures and other instruction
• two-way video conferencing for interactive learning
• email and other messaging tools for communication
• interactive web apps for formative and collaborative activities
• print and photo/scan for handwritten work
• home-based assessment.

To fully participate in ANU learning, students need:

• A computer or laptop. Mobile devices may work well but in some situations a computer/laptop may be more appropriate.
• Webcam
• Speakers and a microphone (e.g. headset)
• Reliable, stable internet connection. Broadband recommended. If using a mobile network or wi-fi then check performance is adequate.
• Suitable location with minimal interruptions and adequate privacy for classes and assessments.
• Printing, and photo/scanning equipment

For more information please see https://www.anu.edu.au/students/systems/recommended-student-system-requirements

Staff Feedback

Students will be given feedback in the following forms in this course:

• Written comments
• Verbal comments
• Feedback to the whole class, to groups, to individuals, focus groups

Student Feedback

ANU is committed to the demonstration of educational excellence and regularly seeks feedback from students. Students are encouraged to offer feedback directly to their Course Convener or through their College and Course representatives (if applicable). The feedback given in these surveys is anonymous and provides the Colleges, University Education Committee and Academic Board with opportunities to recognise excellent teaching, and opportunities for improvement. The Surveys and Evaluation website provides more information on student surveys at ANU and reports on the feedback provided on ANU courses.

Class Schedule

Week/Session	Summary of Activities	Assessment
1	Lecture: Introduction to the coursePractical: How to read and write for quantitative biologists	Journal papers and groups allocated for week 3
2	Lecture: How to present to scientific audiencesPractical: Confronting models with data	Assessments 1 (quiz on week 1 topic)
3	Lecture: Experimental design for quantitative biologistsPractical: Presentations	Assessments 2 (quiz on week 2 topic) & 3 (presentations)
4	Lecture: Crash course in programmingPractical: Programming (continued)	Outline of assignment 1 given
5	Lecture: Theoretical models (what is theory and how do we use it?)Practical: Implementation of numerical models	Assessment 4 (quiz on week 4 topic)
6	Lecture: Agent-based modellingPractical: Implementation of agent-based models	Assessment 5 (quiz on pre-class reading)
7	Lecture: Data miningPractical: Working with eBird data	Assignment 1 (assessment 10) dueAssessment 6 (quiz on pre-class reading), outline of assignment 2 given
8	Lecture: Automated data collection methodsPractical: Working with PIT-tag and barcode data	Assessment 7 (quiz on pre-class reading)
9	Lecture: Machine learningPractical: Using machine learning	Assessment 8 (quiz on pre-class reading)
10	Lecture: Deep learningPractical: Using deep learning
11	Lecture: Animal movementPractical: Working with animal movement data	Assessment 9 (quiz on pre-class reading)
12	Lecture: Advanced animal movementPractical: Working with animal movement data	Assignment 2 (assessment 11) due

Tutorial Registration

Please register for tutorials via MyTT

Assessment Summary

Assessment task	Value	Due Date	Return of assessment	Learning Outcomes
Assessment 1	4 %	01/08/2024	01/08/2024	1
Assessment 2	3 %	08/08/2024	08/08/2024	1
Assessment 3	10 %	15/08/2024	15/08/2024	1
Assessment 4	3 %	22/08/2024	22/08/2024	1
Assessment 5	3 %	29/08/2024	29/08/2024	1
Assessment 6	3 %	19/09/2024	19/09/2024	1
Assessment 7	3 %	26/09/2024	26/09/2024	1
Assessment 8	3 %	03/10/2024	03/10/2024	1
Assessment 9	3 %	17/10/2024	17/10/2024	1
Assignment 1	50 %	20/09/2024	30/09/2024	2
Assignment 2	15 %	25/10/2024	05/11/2024	3

* If the Due Date and Return of Assessment date are blank, see the Assessment Tab for specific Assessment Task details

Policies

ANU has educational policies, procedures and guidelines, which are designed to ensure that staff and students are aware of the University’s academic standards, and implement them. Students are expected to have read the Academic Misconduct Rule before the commencement of their course. Other key policies and guidelines include:

• Student Assessment (Coursework) Policy and Procedure
• Special Assessment Consideration Policy and General Information
• Student Surveys and Evaluations
• Deferred Examinations
• Student Complaint Resolution Policy and Procedure

Assessment Requirements

The ANU is using Turnitin to enhance student citation and referencing techniques, and to assess assignment submissions as a component of the University's approach to managing Academic Integrity. For additional information regarding Turnitin please visit the ANU Online website Students may choose not to submit assessment items through Turnitin. In this instance you will be required to submit, alongside the assessment item itself, hard copies of all references included in the assessment item.

Moderation of Assessment

Marks that are allocated during Semester are to be considered provisional until formalised by the College examiners meeting at the end of each Semester. If appropriate, some moderation of marks might be applied prior to final results being released.

Examination(s)

Short quizzes will be given on most weeks at the start of the practical session.

Assessment Task 1

Assessment 1

Short quiz on the content of the reading and writing lecture

Assessment Task 2

Assessment 2

Short quiz on the content of the experimental design lecture

Assessment Task 3

Assessment 3

Short scientific presentations (12 minutes + questions) on a journal paper given in class. Presentation will include powerpoint slides and oral presentation. The lecture of week 3 will provide background on the content and structure of scientific presentations.

Assessment Task 4

Assessment 4

Short quiz on the content of the programming lecture

Assessment Task 5

Assessment 5

Short quiz on pre-class reading of a scientific paper using agent-based modelling

Assessment Task 6

Assessment 6

Short quiz on pre-class reading of a scientific paper using citizen science data

Assessment Task 7

Assessment 7

Short quiz on pre-class reading of a scientific paper using automated tracking methods

Assessment Task 8

Assessment 8

Short quiz on pre-class reading of a scientific paper using machine and/or deep learning

Assessment Task 9

Assessment 9

Short quiz on pre-class reading of a scientific paper on animal movement

Assessment Task 10

Assignment 1

Students will use a function (provided) capable of running agent-based models of disease spread on networks. The function has a number of different parameter options that can be set. Students will need to develop a research question, run simulations to test the question (by changing the parameter values as needed), plot results, and write a short report containing the background (what is the question and why ask it), the method (how was the question answered), and the results (what was the answer). The report should be maximum 2000 words including the main text, figure legends, tables, and references.

Assessment Task 11

Assignment 2

Pair of students will be provided with the background section of a proposal that specifies a research question and organism. Each pair will need to develop the methods section of the proposal, detailing the most appropriate methods for data collection and analysis to ensure that the design will address the aims of the study. The methods section should be a maximum 1500 words including the main text, illustrative figure legends, and references.

Academic Integrity

Academic integrity is a core part of our culture as a community of scholars. At its heart, academic integrity is about behaving ethically. This means that all members of the community commit to honest and responsible scholarly practice and to upholding these values with respect and fairness. The Australian National University commits to embedding the values of academic integrity in our teaching and learning. We ensure that all members of our community understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. The ANU expects staff and students to uphold high standards of academic integrity and act ethically and honestly, to ensure the quality and value of the qualification that you will graduate with. The University has policies and procedures in place to promote academic integrity and manage academic misconduct. Visit the following Academic honesty & plagiarism website for more information about academic integrity and what the ANU considers academic misconduct. The ANU offers a number of services to assist students with their assignments, examinations, and other learning activities. The Academic Skills and Learning Centre offers a number of workshops and seminars that you may find useful for your studies.

Online Submission

You will be required to electronically sign a declaration as part of the submission of your assignment. Please keep a copy of the assignment for your records. Unless an exemption has been approved by the Associate Dean (Education) a submission must be through Turnitin

Hardcopy Submission

For some forms of assessment (hand written assignments, art works, laboratory notes, etc.) hard copy submission is appropriate when approved by the Associate Dean (Education). Hard copy submissions must utilise the Assignment Cover Sheet. Please keep a copy of tasks completed for your records.

Late Submission

Late submission of assessment tasks without an extension are penalised at the rate of 5% of the possible marks available per working day or part thereof. Late submission of assessment tasks is not accepted after 10 working days after the due date, or on or after the date specified in the course outline for the return of the assessment item. Late submission is not accepted for take-home examinations.

Referencing Requirements

Accepted academic practice for referencing sources that you use in presentations can be found via the links on the Wattle site, under the file named “ANU and College Policies, Program Information, Student Support Services and Assessment”. Alternatively, you can seek help through the Students Learning Development website.

Returning Assignments

Assignments will be return via Wattle and email.

Extensions and Penalties

Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure The Course Convener may grant extensions for assessment pieces that are not examinations or take-home examinations. If you need an extension, you must request an extension in writing on or before the due date. If you have documented and appropriate medical evidence that demonstrates you were not able to request an extension on or before the due date, you may be able to request it after the due date.

Resubmission of Assignments

Resubmission of assignments is not permitted.

Privacy Notice

The ANU has made a number of third party, online, databases available for students to use. Use of each online database is conditional on student end users first agreeing to the database licensor’s terms of service and/or privacy policy. Students should read these carefully. In some cases student end users will be required to register an account with the database licensor and submit personal information, including their: first name; last name; ANU email address; and other information. In cases where student end users are asked to submit ‘content’ to a database, such as an assignment or short answers, the database licensor may only use the student’s ‘content’ in accordance with the terms of service — including any (copyright) licence the student grants to the database licensor. Any personal information or content a student submits may be stored by the licensor, potentially offshore, and will be used to process the database service in accordance with the licensors terms of service and/or privacy policy. If any student chooses not to agree to the database licensor’s terms of service or privacy policy, the student will not be able to access and use the database. In these circumstances students should contact their lecturer to enquire about alternative arrangements that are available.

Distribution of grades policy

Academic Quality Assurance Committee monitors the performance of students, including attrition, further study and employment rates and grade distribution, and College reports on quality assurance processes for assessment activities, including alignment with national and international disciplinary and interdisciplinary standards, as well as qualification type learning outcomes. Since first semester 1994, ANU uses a grading scale for all courses. This grading scale is used by all academic areas of the University.

Support for students

The University offers students support through several different services. You may contact the services listed below directly or seek advice from your Course Convener, Student Administrators, or your College and Course representatives (if applicable).

• ANU Health, safety & wellbeing for medical services, counselling, mental health and spiritual support
• ANU Diversity and inclusion for students with a disability or ongoing or chronic illness
• ANU Dean of Students for confidential, impartial advice and help to resolve problems between students and the academic or administrative areas of the University
• ANU Academic Skills and Learning Centre supports you make your own decisions about how you learn and manage your workload.
• ANU Counselling Centre promotes, supports and enhances mental health and wellbeing within the University student community.
• ANUSA supports and represents undergraduate and ANU College students
• PARSA supports and represents postgraduate and research students