Course overview
- Study period
- Semester 2, 2024 (22/07/2024 - 18/11/2024)
- Study level
- Postgraduate Coursework
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- Chemistry & Molec Biosciences
Advanced Genome Informatics will equip students with the knowledge and practical computing skills necessary to undertake a wide range of genome scale analyses using data produced by high-throughput sequencing technologies. The background lectures will introduce current approaches for analysing data including read mapping, de novo assembly, visualization, and phylogenomics. There will be an emphasis in developing good practice in experimental design and understanding the principles that underpin the commonly used bioinformatics analysis tools. Throughout the course students will learn practical genomics in a series of computer-based practicals using real sequence data, unix command-line tools and high performance computing resources.
Welcome to Advanced Genome Informatics, a dynamic and engaging bioinformatics course designed to plunge you into the world of high-throughput genomic sequence data analysis. Get ready to roll up your sleeves and dive into hands-on experience that will empower you with essential unix command-line skills. Through a series of interactive modules, led by expert bioinformatics researchers, you'll stay at the forefront of the latest trends in genomics.
Imagine being able to navigate and manipulate the vast oceans of genomic data with confidence—this course will make that a reality. Each week, you'll participate in combined lecture and practical sessions where theoretical concepts meet real-world applications. These sessions will be packed with computer exercises on high-performance computing resources, ensuring you gain practical knowledge of current bioinformatics methods.
No prior knowledge of the unix command-line environment? No problem! We'll start from the basics and build your skills progressively. By the end of the course, you'll be equipped to tackle diverse bioinformatics projects with proficiency. Join us on this exciting journey and become a part of the future of genomics research.
Course requirements
Assumed background
This course is part of the Masters in Bioinformatics. It is assumed that students will undertake this course after completing the first semester of the Masters programme. Students wishing to take this course in isolation without first completing BINF6000 and BINF6001 should contact the course coordinator before enrolling.
Prerequisites
You'll need to complete the following courses before enrolling in this one:
BINF6000
Companion or co-requisite courses
You'll need to complete the following courses at the same time:
BINF7000
Course contact
Course staff
Lecturer
Timetable
The timetable for this course is available on the UQ Public Timetable.
Additional timetable information
Check your online timetable regularly.
Aims and outcomes
Advanced Genome Informatics will equip students with the knowledge and practical computing skills necessary to undertake a wide range of genome scale analyses using data produced by next generation sequencing (NGS) technologies. The background lectures will introduce current approaches for analyzing genome and transcriptome data including read mapping, de novo assembly, visualization, and phylogenomics. There will be an emphasis in developing good practice in experimental design and understanding the principles that underpin the commonly used analysis tools.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
Appraise the theory and practice of genome informatics and be prepared to apply these methods to address current problems in the field.
LO2.
Compare the different types of available genomic and transcriptomic data and critique the general approaches used to analyse these.
LO3.
Examine the principles of sequence alignment to the practical problem of mapping reads to a reference sequence.
LO4.
Judge the approaches required for the analysis of metagenomic data.
LO5.
Appraise the principles underpinning common de novo assembly approaches.
LO6.
Explain the approaches required for phylogenomic analysis of sequence data.
LO7.
Describe the approaches required for genomic analysis and functional annotation of human genomic sequence data.
Assessment
Assessment summary
Category | Assessment task | Weight | Due date |
---|---|---|---|
Computer Code, Paper/ Report/ Annotation |
ASSESSMENT 1: Read mapping exercise
|
20% |
23/08/2024 2:00 pm |
Paper/ Report/ Annotation |
ASSESSMENT 2: Human Genomics Analysis
|
30% |
16/09/2024 2:00 pm |
Paper/ Report/ Annotation, Presentation |
ASSESSMENT 3: De novo assembly and phylogenomics
|
30% |
10/10/2024 2:00 pm |
Paper/ Report/ Annotation |
ASSESSMENT 4: Metagenome Analysis
|
20% |
24/10/2024 2:00 pm |
A hurdle is an assessment requirement that must be satisfied in order to receive a specific grade for the course. Check the assessment details for more information about hurdle requirements.
Assessment details
ASSESSMENT 1: Read mapping exercise
- Hurdle
- Mode
- Oral, Written
- Category
- Computer Code, Paper/ Report/ Annotation
- Weight
- 20%
- Due date
23/08/2024 2:00 pm
- Learning outcomes
- L01, L02, L03
Task description
Students will submit a short report about read-mapping analyses with real high-throughput sequencing data. A working script that includes unix commands used to undertake the read-mapping analysis forms part of the submission.
Feedback on the script and other command-line specific tasks within the assessment is designed to help students assess their competency in practical aspects of using the command-line environment to manipulate high-throughput sequence data and perform read-mapping experiments. The practical skills developed in Module 1 and Assessment 1 are important for successfully completing the remainder of the coursework and assessment items. Working on the command-line has a steep learning curve, similar to learning a new language, and the relative weighting of tasks within this assessment ensures that students are not penalised if they are relatively new to the command-line environment.
Use of Artificial Intelligence (AI):
Artificial Intelligence (AI) provides emerging tools that may support students in completing this assessment task. Students may appropriately use AI in completing this assessment task.. Students must clearly reference any use of AI in each instance.
A failure to reference generative AI use may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
Submit your report through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
ASSESSMENT 2: Human Genomics Analysis
- Hurdle
- Mode
- Written
- Category
- Paper/ Report/ Annotation
- Weight
- 30%
- Due date
16/09/2024 2:00 pm
- Other conditions
- Student specific.
- Learning outcomes
- L01, L03, L07
Task description
Laboratory report assessing your ability to detect and analyse germline and somatic mutations from human cancer genome datasets and synthesise information around their potential impact and implications for disease. Students will prepare a laboratory report using simulated genome data and bioinformatics tools provided on the binf-training high performance computer, including:
A) a summary description of the data using bioinformatics methods;
B) an analysis of the germline variants within the genome data and interpretation of these findings; and
C) an analysis of the somatic point mutations and rearrangements present in the tumour sample and interpretation of these findings.
Use of Artificial Intelligence (AI):
This assessment task evaluates students' abilities, skills and knowledge without the aid of generative Artificial Intelligence (AI). Students are advised that the use of AI technologies to develop responses is strictly prohibited and may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
Submit your report through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
ASSESSMENT 3: De novo assembly and phylogenomics
- Hurdle
- Mode
- Oral, Written
- Category
- Paper/ Report/ Annotation, Presentation
- Weight
- 30%
- Due date
10/10/2024 2:00 pm
- Learning outcomes
- L01, L05, L06
Task description
Task Description:
Students will be given a real set of high-throughput sequencing data and will be required to undertake 1) de novo assembly, 2) assessment of assembly quality, 3) ab initio gene prediction, and 4) phylogenomic analyses.
The assessment will consist of two components:
(A) a short video (oral) presentation
(B) a brief technical report with recommendation(s)
Complete guidelines for preparing and submitting the video presentation and the technical report will be given on Learn.UQ.
Use of Artificial Intelligence (AI):
This assessment task evaluates students' abilities, skills and knowledge without the aid of generative Artificial Intelligence (AI). Students are advised that the use of AI technologies to develop responses is strictly prohibited and may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
Submit your video and report through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
ASSESSMENT 4: Metagenome Analysis
- Hurdle
- Mode
- Written
- Category
- Paper/ Report/ Annotation
- Weight
- 20%
- Due date
24/10/2024 2:00 pm
- Learning outcomes
- L01, L04
Task description
Students will analyse and interpret metagenomic sequence data in the context of real-world scenarios. Analysis will include sequence simulation, sequence quality control, taxonomic assignment, and annotation using both web-based and command-line tools. Students will prepare answers to a problem as well as a report detailing the bioinformatic analyses of a viral metagenome and a description of the viral community. Full guidelines for the project report requirements will be given on Learn.UQ.
Use of Artificial Intelligence (AI):
This assessment task evaluates students' abilities, skills and knowledge without the aid of generative Artificial Intelligence (AI). Students are advised that the use of AI technologies to develop responses is strictly prohibited and may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.Submission guidelines
Submit your report through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1Submission via Turnitin portal on Blackboard @ Learn.UQ
Deferral or extension
You may be able to apply for an extension.
Applications for Extensions
Information on applying for an extension can be found here: my.UQ Applying for an extension.
Extension applications must be received by the assessment due date and time.
If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.
Prolonged Absence
If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.
Extensions with Student Access Plans (SAP)
For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
Course grading
Full criteria for each grade is available in the Assessment Procedure.
Grade | Description |
---|---|
1 (Low Fail) |
Absence of evidence of achievement of course learning outcomes. Course grade description: Some engagement with the assessment tasks; however no demonstrated evidence of understanding of the concepts in the field of study The minimum percentage required for this grade is: 0% |
2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: Inability to apply knowledge and skills The minimum percentage required for this grade is: 30% |
3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: Emerging ability to apply knowledge and skills The minimum percentage required for this grade is: 45% |
4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: Acceptable application of knowledge and skills The minimum percentage required for this grade is: 50% |
5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: Effective application of knowledge and skills The minimum percentage required for this grade is: 65% |
6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: Extensive application of knowledge and skills The minimum percentage required for this grade is: 75% |
7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: Original, novel and/or creative application of knowledge and skills The minimum percentage required for this grade is: 85% |
Additional course grading information
Assessment Hurdles
In order to pass this course, you must meet ALL of the following requirements (if you do not meet these requirements, the maximum grade you will receive will be a 3):
1. You must obtain an overall mark of 50% or more; and
2. You must achieve a minimum of 40% in each assessment item; andᅠ
3. You must complete and submit ALL assessment items.
Supplementary assessment
Supplementary assessment is available for this course.
Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply.
Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.
If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.
Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes.
To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment.
Additional assessment information
Assessment Submission
It is the responsibility of the student to ensure the on time, correct and complete submission of all assessment items.
Please ensure you receive and save the submission confirmation for all submitted items, you may be asked to produce this as evidence of your submission.
Turnitin
By submitting work through Turnitin you are deemed to have accepted the following declaration “I certify that this assignment is my own work and has not been submitted, either previously or concurrently, in whole or in part, to this University or any other educational institution, for marking or assessment”.
All students must ensure they receive their Turnitin receipt on submission of any assessments. A valid Turnitin receipt will be the only evidence accepted if one or more of your submissions are missing. Without evidence, the assessment will receive the standard late penalty, or after seven days, will receive zero. In the case of a Blackboard outage, please contact the Course Coordinator as soon as possible to confirm the outage with ITS.
Assessment/Attendance
Please notify your Course Coordinator as soon as you become aware of any issue that may affect your ability to meet the assessment/attendance requirements of the course. The my.UQ website and the Electronic Course Profile (ECP) for your course also provide information about your course requirements, the rules associated with your courses and services offered by the University.
A note for repeating students in this course
Any student who enrols in a course must not be given exemption or partial credit from their previous attempt(s) for any individual piece of assessment. Instead, the student must successfully complete all of the learning activities and assessment items within the study period of enrolment (PPL Assessment - Procedures Section: Assessment integrity).
If the same assessment item is set from one year to the next, repeating students are allowed to submit the same work they submitted in previous attempts at the course. Where possible SCMB recommends that you use the feedback you received in your last attempt to improve parts of the item where you lost marks. Resubmission of an altered or unaltered assessment item by a repeating student (where the same assessment has been set) will not be considered as self-plagiarism.
Important Note
Turnitin is to be used for assignments/laboratory reports to check for plagiarism. Penalties can be severe for plagiarism.
The University has adopted the following definition of plagiarism: Plagiarism is the act of misrepresenting as one's own original work the ideas, interpretations, words or creative works of another either intentionally or unintentionally. These include published and unpublished documents, designs, music, sounds, images, photographs, computer codes and ideas gained through working in a group. These ideas, interpretations, words or works may be found in print and/or electronic media.
Students are encouraged to read the UQ Academic Integrity and Plagiarism policy at: ppl.app.uq.edu.au/content/3.60.04-student-integrity-and-misconduct
Learning resources
You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.
Library resources
Find the required and recommended resources for this course on the UQ Library website.
Additional learning resources information
Blackboard
Additional material (including the Turnitin portal) may be found on the Blackboard site for BINF7001 at learn.uq.edu.au
Please check the Announcements section of the Blackboard site regularly for information updates.
Learning activities
The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.
Filter activity type by
Please select
Learning period | Activity type | Topic |
---|---|---|
Multiple weeks From Week 1 To Week 4 |
General contact hours |
Module 1: Introduction to the command line and read mapping [SB] Lectorial sessions each week include lectures, practical exercise walk-throughs and independent work on the topic of read-mapping. Includes in-depth introduction to unix command-line. Learning outcomes: L01, L02, L03 |
Multiple weeks From Week 5 To Week 7 |
General contact hours |
Module 2: Human genomics and mutation [AE] Lectorial sessions each week include lectures, practical exercise walk-throughs and independent work on the topic of human genomics and mutation. Learning outcomes: L01, L02, L03, L07 |
Multiple weeks From Week 8 To Week 10 |
General contact hours |
Module 3: De novo genome assembly and phylogenomics [CC] Lectorial sessions each week include lectures, practical exercise walk-throughs and independent work on the topic of de novo assembly and phylogenomics. Learning outcomes: L01, L02, L05, L06 |
Multiple weeks From Week 11 To Week 13 |
General contact hours |
Module 4: Metagenomics [PH] Lectorial sessions each week include lectures, practical exercise walk-throughs and independent work on the topic of metagenomics. Learning outcomes: L01, L02, L04 |
Policies and procedures
University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:
- Student Code of Conduct Policy
- Student Integrity and Misconduct Policy and Procedure
- Assessment Procedure
- Examinations Procedure
- Reasonable Adjustments - Students Policy and Procedure
Learn more about UQ policies on my.UQ and the Policy and Procedure Library.