Biological research techniques are changing rapidly, and each year, we learn about new ways of collecting biological data, including genomic, phenotypic, ecological and environmental data. New data often require new methods of analysis, or novel applications of existing techniques. At the same time, novel mathematical models and theories are required to explain emerging patterns in biological data. Students will learn the latest methods, models and theories for organising, analysing and interpreting biological data.

Learning Outcomes

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. Identify analyses appropriate for different types of data, and explain their theoretical foundations.
2. Describe, present, and critically evaluate analytical methods, models and theories used in published research, and identify, where relevant, more appropriate alternatives.
3. Apply and extend analytical methods, models and theories to biological datasets.

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	Review of Probability distributions, example from high-throughput sequencing	Assignment 1
2	Review of matrices, eigenvectors and eigenvalues. Introduction to Markov chains.	Assignments 1&2
3	More Markov chains. Continuous-time Markov models and Rate matrices	Assignments 1&2
4	Genomics 1: DNA sequencing and genome assembly	Assignment 3
5	Genomics 2: Genome assembly	Assignments 3
6	Genomics 3: Meta-genomics	Assignments 3
7	Multiple sequence alignment	Assignments 4
8	Building phylogenetic tree I	Assignments 4
9	Building phylogenetic tree II	Assignments 4
10	Graduate study group with focus on genomics and genome assembly	Assignments 5&8
11	Graduate study group with focus on de novo gene evolution	Assignments 6&8
12	Graduate study group with focus on SARS-COV2 biology and phylogenetics	Assignments 5&8

Tutorial Registration

Please register for tutorials via email

Assessment Summary

Assessment task	Value	Due Date	Return of assessment	Learning Outcomes
Assignment 1	10 %	07/08/2020	21/08/2020	1
Assignment 2	15 %	21/08/2020	04/09/2020	1
Assignment 3	25 %	11/09/2020	25/09/2020	1,3
Assignment 4	25 %	16/10/2020	30/10/2020	1,3
Assignment 5	5 %	15/10/2020	29/10/2020	2,3
Assignment 6	5 %	22/10/2020	05/10/2020	2,3
Assignment 7	5 %	29/10/2020	12/11/2020	2,3
Assignment 8	10 %	13/11/2020	27/11/2020	2,3

* 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.

Assessment Task 1

Assignment 1

This will be a written assignment including R scripts that analyze the presented data. The assignment will require basic fluency in R.

Assessment Task 2

Assignment 2

This will be a written assignment including R scripts that analyze the presented data. The assignment will require basic fluency in R.

Assessment Task 3

Assignment 3

This will be a written assignment that includes a significant project programmatic component. The minimum total amount of words is 1500. In this assignment, you will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives.

Assessment Task 4

Assignment 4

This will be a written assignment that includes a significant project programmatic component. The minimum total amount of words is 1500. In this assignment, you will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives.

Assessment Task 5

Assignment 5

This will be a graduate seminar on genomics and genome assembly. This assignment will be in class participation including discussion groups and multiple choice questions. You will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives. If in class participation is not possible a 300 words assay on the topic can be handed in the same day as replacement. Please email the course convenor about this option.

Assessment Task 6

Assignment 6

This will be a graduate seminar on de novo gene evolution. This assignment will be in class participation including discussion groups and multiple choice questions. You will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives. If in class participation is not possible a 300 words assay on the topic can be handed in the same day as replacement. Please email the course convenor about this option.

Assessment Task 7

Assignment 7

This will be a graduate seminar on SARS-COV2 biology and phylogenetic. This assignment will be in class participation including discussion groups and multiple choice questions. You will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives. If in class participation is not possible a 300 words assay on the topic can be handed in the same day as replacement. Please email the course convenor about this option.

Assessment Task 8

Assignment 8

This will a critical assay on one of the following research areas including detailed literature evaluations. The research areas are I) genomics and genome assembly, II) de novo gene evolution and III) SARS-COV2 biology and phylogenetics. You cannot choose a topic you already handed in an assay for. If you have no topic left the convenor will provide you with a new topic and reading list. The assay is a 600 word assay. About half of the assay should cover the literature summary of the provided reading list. About half of the assay should be a detailed discussion on how one of the subject areas covered in module 1-3 relates to the specific research area. This should be a in depth discussion on one topic. You will critically evaluate analytical methods, models and theories in published research. Where relevant you are encouraged to identify and suggest more appropriate alternatives.

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

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