- Class Number 8585
- Term Code 3060
- Class Info
- Unit Value 6 units
- Mode of Delivery In Person
- Dr Xia Hua
- Dr Conrad Burden
- Dr Xia Hua
- Class Dates
- Class Start Date 27/07/2020
- Class End Date 30/10/2020
- Census Date 31/08/2020
- Last Date to Enrol 03/08/2020
The course begins with a detailed discussion of sequence alignment algorithms that are critical for assessing the relatedness of DNA, RNA and amino acid sequences. We then proceed to studying Markov chains and hidden Markov models as important examples of biological models for such sequences. The main algorithms and several applications will be explained. Finally, a broad range of examples of applications of mathematics in biology, both at the molecular and macroscopic level, will be given. These may include current research being done at the ANU and readings published research papers. The course is accompanied by computing exercises which explore the implementation of algorithms and their assessment though analysis of synthetic data.
This course is co-taught with undergraduate students but assessed separately, with extra assignment questions set at an advanced level.
Upon successful completion, students will have the knowledge and skills to:
- Explain thoroughly models for the evolution and comparison of biological sequences and their applications.
- Demonstrate a deep understanding of probabilistic concepts such as probability spaces, conditional probability, Markov chains, and stationary distributions.
- Demonstrate a deep understanding of the main principles of mathematical modelling in biology and the capacity to construct mathematical models.
Students will be given feedback in the following forms in this course:
- written comments
- verbal comments
- feedback to whole class, groups, individuals, focus group etc
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.
|Week/Session||Summary of Activities||Assessment|
|1||DNA and protein sequences: Alignments||Assignment 1 and final exam|
|2||DNA and protein sequences: Alignments||Assignment 1 and final exam|
|3||DNA and protein sequences: Alignments||Assignment 1 and final exam|
|4||DNA and protein sequences: Markov Models||Assignment 2 and final exam|
|5||DNA and protein sequences: Markov Models||Assignment 2 and final exam|
|6||DNA and protein sequences: Markov Models||Assignment 2 and final exam|
|7||Mathematical modelling: Epidemiology||Assignment 3 and final exam|
|8||Mathematical modelling: Epidemiology||Assignment 3 and final exam|
|9||Mathematical modelling: How a liver works||Assignment 3 and final exam|
|10||Mathematical modelling: How a liver works||Assignment 4 and final exam|
|11||Phylogenetic trees||Assignment 4 and final exam|
|12||Phylogenetic trees||Assignment 4 and final exam|
|Assessment task||Value||Due Date||Return of assessment||Learning Outcomes|
|Assignment 1||15 %||14/08/2020||21/08/2020||1,2,3|
|Assignment 2||15 %||04/09/2020||25/09/2020||1,2,3|
|Assignment 3||15 %||09/10/2020||16/10/2020||1,2,3|
|Assignment 4||15 %||30/10/2020||06/11/2020||1,2,3|
|Final written exam||40 %||05/11/2020||03/12/2020||1,2,3|
* If the Due Date and Return of Assessment date are blank, see the Assessment Tab for specific Assessment Task details
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:
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 Academic Integrity . In rare cases where online submission using Turnitin software is not technically possible; or where not using Turnitin software has been justified by the Course Convener and approved by the Associate Dean (Education) on the basis of the teaching model being employed; students shall submit assessment online via ‘Wattle’ outside of Turnitin, or failing that in hard copy, or through a combination of submission methods as approved by the Associate Dean (Education). The submission method is detailed below.
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.
Please note, that where a date range is used in the Assessment Summary in relation to exams, the due date and return date indicate the approximate timeframe in which the exam will be held and results returned to the student (official end of Semester results released on ISIS). Students should consult the course wattle site and the ANU final examination timetable to confirm the date, time and venue of the exam.
Assessment Task 1
Learning Outcomes: 1,2,3
Written assignment, value 15%, due 9 August. Masters level students will complete extra, more difficult questions in addition to those set for the co-taught undergraduate course MATH2307.
Assessment Task 2
Learning Outcomes: 1,2,3
Written assignment, value 15%, due 30 August. Masters level students will complete extra, more difficult questions in addition to those set for the co-taught undergraduate course MATH2307.
Assessment Task 3
Learning Outcomes: 1,2,3
Written assignment, value 15%, due 4 October. Masters level students will complete extra, more difficult questions in addition to those set for the co-taught undergraduate course MATH2307.
Assessment Task 4
Learning Outcomes: 1,2,3
Written assignment, value 15%, due 25 October. Masters level students will complete extra, more difficult questions in addition to those set for the co-taught undergraduate course MATH2307.
Assessment Task 5
Learning Outcomes: 1,2,3
Final written exam
48 hour final take-home exam during exam period; value 40%, A minimum of 16 out of 40 is required to pass the course.
The date range in the Assessment Summary indicates the start of the end of semester exam period and the date official end of semester results are released on ISIS. Please check the ANU final Examination Timetable http://www.anu.edu.au/students/program-administration/assessments-exams/examination-timetable to confirm the date, time and location exam.
Academic integrity is a core part of the ANU culture as a community of scholars. At its heart, academic integrity is about behaving ethically, committing to honest and responsible scholarly practice and upholding these values with respect and fairness.
The ANU commits to assisting all members of our community to 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 be familiar with the academic integrity principle and Academic Misconduct Rule, 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 Academic Misconduct Rule is in place to promote academic integrity and manage academic misconduct. Very minor breaches of the academic integrity principle may result in a reduction of marks of up to 10% of the total marks available for the assessment. The ANU offers a number of online and in person services to assist students with their assignments, examinations, and other learning activities. Visit the Academic Skills website for more information about academic integrity, your responsibilities and for assistance with your assignments, writing skills and study.
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) submission must be through Turnitin.
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 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 5 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.
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.
Assignments will be graded and returned via Wattle.
Extensions and Penalties
Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure. Extensions may be granted 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.
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
Dr Xia Hua
Dr Conrad Burden