The aim of this course is to teach Genomics, spanning ecosystems, evolution, host-microbe, assembly, epigenomics, and transcriptomics. We consider plants, microbes, and animals from model organisms to foundation species. The course will cover recent developments in 3rd gen, long read, genomics with labs applied to soils, trees and insect gene expression. Students taking this course will develop skills in experimentation and analysis within the context of learning about biology including: gene regulation, genome evolution, complex adaptive and quantitative traits, and genome engineering with synthetic biology.
Learning Outcomes
Upon successful completion, students will have the knowledge and skills to:
- Describe recent advances in genome assembly, (epi)genomic variation, SV/SNPs,and transcriptomics,
- Demonstrate an understanding of third gen genomics technologies and illustrate how they are used for genome assembly, variant identification/typing, annotation and expression
- Obtain and analyse information and data relating to specific genetic variation along the genome, population genetic variation among samples across the genome
- Perform a range of practical techniques including DNA extraction, library preparation, and 3rd gen sequencing
- Design a set of experiments to address a particular biological question.
Research-Led Teaching
The lecture material draws from new research providing current knowledge and examples of the fundamentals of genome biology. This exposes students to present-day techniques and innovation, which connects them to current ideas in the science field. Furthermore, the students have the opportunity to engage with a range of science, allowing an environment for students to make connections for potential future research projects.
Additionally, the lectures complement the practical component of the course, which aims to foster and teach skills required in a research environment. These skills range from basic practical techniques of sampling, DNA extraction, libraries and analysis, to learning how to critically discuss the theory behind the science.
Field Trips
A hike up Black Mountain to the ring track will take place to discuss and demonstrate landscape sampling design.
HPO will be a lab based DNA extraction, library, sequencing and analysis of your own samples!
Recommended Resources
Course specific resources:
- dynamic gDoc lab manuals including analysis
Other requirements:
Whether you are on campus or studying online, there are a variety of online platforms you will use to participate in your study program. These could include videos 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/or photo/scan for handwritten work and drawings, and home-based assessment.
ANU outlines recommended student system requirements to ensure you are able to participate fully in your learning. Other information is also available about the various Learning Platforms you may use.
Staff Feedback
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
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). 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.
Other Information
Honours pathway option (HPO)
The HPO consists of inquiry-learning, practical exercises on molecular techniques. The additional practical exercises provide experience of extra laboratory skills, an opportunity to develop more complex data analysis and interpretive skills and an extension of the theory taught in the course.
The marking for the HPO is simply a pass for completing it.
Class Schedule
| Week/Session | Summary of Activities | Assessment |
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| 1 | Week 1 (23-27 Feb)
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| 2 | Week 2 (2-6 Mar)
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| 3 | Week 3 (9-12 Mar)
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quiz in class 8% |
| 4 | Week 4 (16-20 Mar)
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| 5 | Week 5 (16-20 Mar)
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lab report due |
| 6 | Week 6 (23-27 Mar)
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Mid-semester Exam |
| 7 | Week 7 (30 Mar- 3 Apr)
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| 8 | Week 8 (20 -24 Apr)
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| 9 | Week 9 (27 Apr - 1 May)
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| 10 | Week 10 (4-8 May)
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2nd lab report due |
| 11 | Week 11 (18-22 May)
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| 12 | Week 12 (25-29 May)
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final exam quiz |
Tutorial Registration
ANU utilises MyTimetable to enable students to view the timetable for their enrolled courses, browse, then self-allocate to small teaching activities / tutorials so they can better plan their time. Find out more on the Timetable webpage.Assessment Summary
| Assessment task | Value | Learning Outcomes |
|---|---|---|
| initial quiz | 8 % | 1,2 |
| Lab I Assignment: landscape genomics | 20 % | 1,2,3,4,5 |
| Mid-semester Assessment | 12 % | 1,2 |
| Lab 2 Assignment: differential abundance | 20 % | 1,2,3,4,5 |
| Class presentation | 20 % | 1,2,3,4,5 |
| Final Exam | 20 % | 1,2 |
* 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 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
- Extenuating Circumstances Application
- Student Surveys and Evaluations
- Deferred Examinations
- Student Complaint Resolution Policy and Procedure
- Code of practice for teaching and learning
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 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 ‘Canvas’ 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.
Participation
It is expected that all students attend and participate in all labs. Because labs are central to the course, attendance and participation is required to be eligible to submit the associated assessment items. Attendance at lectures is also strongly recommended.
Examination(s)
No final exam, just online in class final quiz
Assessment Task 1
Learning Outcomes: 1,2
initial quiz
This is an early short quiz based on lectures to get feedback. 8%
Assessment Task 2
Learning Outcomes: 1,2,3,4,5
Lab I Assignment: landscape genomics
The objective of this assignment is for you to demonstrate your understanding of the principles of sampling individuals, Nanopore sequencing, read mapping and sample identification. This assignment also aims to assess your proficiency in science writing, data analysis, and critical evaluation of your results in conjunction with the literature, experiment design and lateral thinking. 20%
Assessment Task 3
Learning Outcomes: 1,2
Mid-semester Assessment
This short multiple choice quiz test is for you to demonstrate your understanding of the first block of lectures.
Week 6
12%
Assessment Task 4
Learning Outcomes: 1,2,3,4,5
Lab 2 Assignment: differential abundance
The objective of this assignment is for you to demonstrate your understanding of metagenome biology and RNA seq. you will analyze data from soil metagenomics and RNAseq studies and determine differential abundance This assignment also aims to assess your proficiency in science writing, data analysis, and critical evaluation of your results in conjunction with the literature, experiment design and lateral thinking. 20%
Assessment Task 5
Learning Outcomes: 1,2,3,4,5
Class presentation
You have 5min, individually or as part of a group, to present your idea for a startup genomics company and how to address ethical questions from users and the public. 20%
Assessment Task 6
Learning Outcomes: 1,2
Final Exam
Final Exam in class quiz covering 2nd half of the course. 20%
Academic Integrity
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.
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) submission must be through Turnitin.
Hardcopy Submission
No hard copy submissions accepted
Late Submission
Late submission permitted. 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
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. Any use of artificial intelligence must be properly referenced. Failure to properly cite use of Generative AI will be considered a breach of academic integrity.
Returning Assignments
Marks and feedback of lab report will be available on Turnitin about 2 weeks after submission. Quiz results will likely be returned the same day
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 accepted.
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 Accessibility 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 supports you make your own decisions about how you learn and manage your workload.
- ANU Counselling promotes, supports and enhances mental health and wellbeing within the University student community.
- ANUSA supports and represents all ANU students
Convener
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Prof Justin Borevitz
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Instructor
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AsPr Hardip Patel
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Demonstrator
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Sarah Jackson
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