- Class Number 2950
- Term Code 3330
- Class Info
- Unit Value 6 units
- Mode of Delivery In Person
- Dr Xia Hua
- Dr Xia Hua
- Class Dates
- Class Start Date 20/02/2023
- Class End Date 26/05/2023
- Census Date 31/03/2023
- Last Date to Enrol 27/02/2023
This course begins with a brief review of some of the areas of probability and statistics needed for applications to bioinformatics problems. Typical problems addressed by bioinformaticians are identifying functionally different parts of a genome, searching DNA or protein databases to find sequences which are functionally similar to a given query sequence, or inferring the relatedness of different species by measuring the similarity of their genomes. The course will cover the mathematical theory behind algorithms commonly used by biologists and also give examples of current research.
Note: This is an Honours Pathway Course. It emphasises mathematical rigour for a range of advanced Bioinformatics topics.
Upon successful completion, students will have the knowledge and skills to:
On satisfying the requirements of this course, students will have the knowledge and skills to:
1. Explain the fundamental concepts of a special topic in bioinformatics and its role in modern mathematics and applied contexts.
2. Demonstrate accurate and efficient use of specific bioinformatics techniques.
3. Demonstrate capacity for mathematical reasoning through analysing, proving and explaining concepts from bioinformatics.
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.
- 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
Students will be given feedback in the following forms in this course:
- written comments on assignments
- verbal comments in answer to questions in lectures and tutorials
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). Feedback can also be provided to Course Conveners and teachers via the Student Experience of Learning & Teaching (SELT) feedback program. SELT surveys are confidential and also provide the Colleges and ANU Executive with opportunities to recognise excellent teaching, and opportunities for improvement.
|Week/Session||Summary of Activities||Assessment|
|1||Review of probability and statistics||Assignment 1 & final exam|
|2||Analysis of a single DNA sequence||Assignment 1 & final exam|
|3||Analysis of a single DNA sequence||Assignment 1 & final exam|
|4||Analysis of a single DNA sequence||Assignment 2 & final exam|
|5||DNA and protein sequence comparison||Assignment 2 & final exam|
|6||DNA and protein sequence comparison||Assignment 2 & final exam|
|7||DNA and protein sequence comparison||Assignment 3 & final exam|
|8||DNA and protein sequence comparison||Assignment 3 & final exam|
|9||Population genetics||Assignment 3 & final exam|
|10||Population genetics||Assignment 4 & final exam|
|11||Population genetics||Assignment 4 & final exam|
|12||Population genetics||Assignment 4 & final exam|
Refer to the ANU Class Timetable (MyTimetable) and the course Wattle site.
|Assessment task||Value||Due Date||Return of assessment||Learning Outcomes|
|Assignment 1||15 %||10/03/2023||24/03/2023||1,2,3|
|Assignment 2||15 %||31/03/2023||14/04/2023||1,2,3|
|Assignment 3||15 %||05/05/2023||19/05/2023||1,2,3|
|Assignment 4||15 %||26/05/2023||09/06/2023||1,2,3|
|Final Exam||40 %||01/06/2023||29/06/2023||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 Integrity Rule before the commencement of their course. Other key policies and guidelines include:
- Academic Integrity Policy and Procedure
- Student Assessment (Coursework) Policy and Procedure
- Special Assessment Consideration Guideline and General Information
- Student Surveys and Evaluations
- Deferred Examinations
- Student Complaint Resolution Policy and Procedure
- Code of practice for teaching and learning
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 Skills website. 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.
In Semester 1 2023, this course is delivered on campus with remote adjustments only for participants with unavoidable travel restrictions/visa delays. Timetabled Lectures and Workshops will also be run as a simultaneous Zoom session to enable remote students to follow in real time and to interact with the lecturer/demonstrator.
Please note, that where a date range is used in the Assessment Summary in relation to exams, the due date and return date for mid-semester exams indicate the approximate timeframe in which the exam will be held; the due and return date for end of semester exams indicate the approximate timeframe in which the exam will be held and the date official end of Semester results are released on ISIS. Students should consult the course wattle site and the ANU final examination timetable to confirm the date, time and mode of the exam.
Assessment Task 1
Learning Outcomes: 1,2,3
Written and R programming problems relating to material covered in Weeks 1 to 3.
Assessment Task 2
Learning Outcomes: 1,2,3
Written and R programming problems relating to material covered in Weeks 4 to 6.
Assessment Task 3
Learning Outcomes: 1,2,3
Written and R programming problems relating to material covered in Weeks 7 to 9.
Assessment Task 4
Learning Outcomes: 1,2,3
Written and R programming problems relating to material covered in Weeks 10 to 12.
Assessment Task 5
Learning Outcomes: 1,2,3
48 hour take-home exam covering all aspects of the course.
The date range 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 mode of the end of semester exam.
Academic integrity is a core part of the ANU culture as a community of scholars. The University’s students are an integral part of that community. The academic integrity principle commits all students to engage in academic work in ways that are consistent with, and actively support, academic integrity, and to uphold this commitment by behaving honestly, responsibly and ethically, and with respect and fairness, in scholarly practice.
The University expects all staff and students to be familiar with the academic integrity principle, the Academic Integrity Rule 2021, the Policy: Student Academic Integrity and Procedure: Student Academic Integrity, and to uphold high standards of academic integrity to ensure the quality and value of our qualifications.
The Academic Integrity Rule 2021 is a legal document that the University uses to promote academic integrity, and manage breaches of the academic integrity principle. The Policy and Procedure support the Rule by outlining overarching principles, responsibilities and processes. The Academic Integrity Rule 2021 commences on 1 December 2021 and applies to courses commencing on or after that date, as well as to research conduct occurring on or after that date. Prior to this, the Academic Misconduct Rule 2015 applies.
The University commits to assisting all students to understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. All coursework students must complete the online Academic Integrity Module (Epigeum), and Higher Degree Research (HDR) students are required to complete research integrity training. The Academic Integrity website provides information about services available to assist students with their assignments, examinations and other learning activities, as well as understanding and upholding academic integrity.
You will be required to agree to a declaration as part of the submission of your assignments, that will record your understanding of ANU academic integrity principles. Please keep a copy of the assignment for your records. MATH3353 does not use Turnitin, having been granted an exemption.
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 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.
The Academic Skills website has information to assist you with your writing and assessments. The website includes information about Academic Integrity including referencing requirements for different disciplines. There is also information on Plagiarism and different ways to use source material.
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.
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 Access 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
Mathematical Biology, Bioinformatics, Biostatistics
Dr Xia Hua