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:

1. Describe recent advances in genome assembly, (epi)genomic variation, SV/SNPs,and transcriptomics,
2. Demonstrate an understanding of third gen genomics technologies and illustrate how they are used for genome assembly, variant identification/typing, annotation and expression
3. Obtain and analyse information and data relating to specific genetic variation along the genome, population genetic variation among samples across the genome
4. Perform a range of practical techniques including DNA extraction, library preparation, and 3rd gen sequencing
5. 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 trip to the National Arboretum STEP forest so see planted diversity on ecological gradients. Topics will also be covered in class so you can do sampling yourself including plant and/or soil microbial samples.

Recommended Resources

Recommended student system requirements 

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

• email for communication
• dynamic gDoc lab manuals including analysis
• 
  

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.

Staff Feedback

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

• Written comments
• Feedback to the whole class or to 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.

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.

Please note, that where there are multiple assessment tasks of the same type, e.g weekly quizzes, a date range is used in the Assessment Summary. The first date is the approximate due date of the first task, the return date is the approximate return date for the final task. Further information is provided in the assessment section of the class summary, and details are provided on the course wattle site

Class Schedule

Week/Session	Summary of Activities	Assessment
1	Week 1Lecture: Course OverviewLectures: Genes and Genomes	https://docs.google.com/spreadsheets/d/1A-wff70wQvEzhdS29iPtyUc5Lyi1YiKS/edit?gid=1912781595#gid=1912781595
2	Week 2Lectures: MicrobiomeLab I: microbiome
3	Week 3Lectures: Genome AssemblyLab I: microbiome
4	Week 4Lectures: structural variationLab I: microbiome
5	Week 5Lectures: Populations and Natural VariationLab I: microbiome
6	Week 6lectures: Phenomics & GWAS	Lab I Assignment DueMid-semester Exam Friday
7	Mid-semester Break
8	Week 7Lectures: Human/Aboriginal GenomicsLab II: landscape genomics
9	Week 8Lectures: EpigenomicsLab II: landscape genomics
10	Week 9Lectures: transcriptomicsLab II: landscape genomics
11	Week 10Lectures: single cell/eQTLLab II: landscape genomics
12	Week 11Lectures: Synthetic Biology	Lab II Assignment Due
13	Week 12Student Final Presentations	student presentations

Tutorial Registration

No need to register for tutorials.

Assessment Summary

Assessment task	Value	Learning Outcomes
Mid-semester Assessment	20 %	1, 2
Lab I Assignment: soil genomics	20 %	1, 2, 3, 4, 5
Lab II Assignment: landscape genomics	20 %	1, 2, 3, 4, 5
Class presentation	20 %	1, 2, 3, 4, 5
Final Exam (2nd half of the course)	20 %	1, 2, 6

* 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.

Participation

Attendance at all labs is compulsory. Attendance at lectures is also compulsory. Talk with me if you can't make most lectures.

Examination(s)

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 venue of the exam.

Assessment Task 1

Mid-semester Assessment

This short multiple choice mid-term test is for you to demonstrate your understanding of the first block of lectures.

Week 6

Assessment Task 2

Lab I Assignment: soil genomics

The objective of this assignment is for you to demonstrate your understanding of metagenome biology. you will sample culture & fractionate, soil and/or rhizosphere DNA for extraction, barcode library and sequencing to classify what the samples are, how they are related and the potentially functionally important differentially abundance microbes. 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.

Assessment Task 3

Lab II Assignment: landscape genomics

The objective of this assignment is for you to demonstrate your understanding of the principles of sampling individuals, DNA extraction, library construction, 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.

Assessment Task 4

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.

Assessment Task 5

Final Exam (2nd half of the course)

This exam consists of multiple choice questions, to demonstrate your understanding of the content and general principles of the course lectures for the 2nd part.

Please check the ANU final Examination Timetable to confirm the date, time and location of the end of semester exam.

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

The ANU uses 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. While the use of Turnitin is not mandatory, the ANU highly recommends Turnitin is used by both teaching staff and students. For additional information regarding Turnitin please visit the ANU Online website.

Hardcopy Submission

Hard copy submissions are not accepted

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

Marks and feedback of assessments 2, 3 and 4 will be available on Turnitin by the specified dates. Marks of assessments 1 and 5 will be be available by the specified dates and students can view and discuss the exam papers with course convener.

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 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 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