Bioinformatics 2: Development & Research (BINF7000)

Course overview

Advanced Bioinformatics equips the student with the interdisciplinary knowledge and skills necessary to meet the data-centred challenges and demands of modern-day biology, with emphasis on genomics. Methods and algorithms for uncovering patterns in biological data of different forms are discussed, and in several cases developed, implemented and applied to representative problems. The student develops both theoretical and practical skills, allowing them to solve real bioinformatics problems by computer programming.

Modern-day biology is increasingly characterised by genome-scale and data-driven approaches. This trend has given rise to the discipline known as bioinformatics: the use of mathematics, statistics and computing to manage, analyse and build models from biological data to solve scientific problems. Present-day bioinformaticians are typically either bio-scientists armed with the methods of computer science, statistics and mathematics, or data analysts intimately acquainted with the nature and challenges of molecular biology. This course aims to cater for the background and needs of both these groups. Moreover, the course is designed to leverage synergies between the two groups. The course aims to instil

• An appreciation and understanding of a range of computational and statistical applications in biology involving the processing, analysis of and model-building from genomic data and other biological data
• The knowledge and skills (both theoretical and practical) required to develop computational methods and tools, to make informed, data-driven discoveries in molecular biology

Following on from an introductory course, ﾠthe course presents key methodological concepts in bioinformatics, in the context of the problems to which they are suited. The course has two major parts, namely

• bioinformatics methodology, and
• bioinformatics research and applications.

Learning activities allow the student to develop a conceptual understanding of common bioinformatics methods. Hands-on computer programming is used to strengthen a detailed understanding of bioinformatics algorithms, and to explore and evaluate their value on representative types of biological ﾠdata.

Course requirements

Assumed background

Basic programming skills in Python. Basic knowledge and interest in molecular biology.

Prerequisites

You'll need to complete the following courses before enrolling in this one:

BINF6000

Recommended prerequisites

We recommend completing the following courses before enrolling in this one:

CSEE7030

Companion or co-requisite courses

You'll need to complete the following courses at the same time:

BINF7001

Incompatible

You can't enrol in this course if you've already completed the following:

BIOL3014 or SCIE3100

Jointly taught details

This course is jointly-taught with:

Lectures, assessment and practicals may be shared between SCIE3100 and BINF7000.

Course contact

Course staff

Timetable

The timetable for this course is available on the UQ Public Timetable.

Aims and outcomes

The growth and diversity of biological data threatens to outstrip our ability to analyse and understand it. This course aims to equip students with an advanced understanding of current computational methods to expand the knowledge of molecular biology.

Learning outcomes

After successfully completing this course you should be able to:

Assessment

Assessment summary

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

Assignment 1: Probabilistic data analysis

• Hurdle
• Team or group-based
• Online

Mode

Written

Category

Computer Code, Practical/ Demonstration, Tutorial/ Problem Set

Weight

20%

Due date

30/08/2024 2:00 pm

Other conditions

Student specific.

See the conditions definitions

Task description

Hurdle requirements

Submission guidelines

Online submission as directed on the assignment specification available online from the course site.

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.

Assignment 2: Machine learning on DNA elements

• Hurdle
• Team or group-based
• Online

Mode

Written

Category

Computer Code, Practical/ Demonstration, Tutorial/ Problem Set

Weight

20%

Due date

20/09/2024 2:00 pm

Other conditions

Student specific.

See the conditions definitions

Task description

Hurdle requirements

Submission guidelines

Online submission as directed on the assignment specification

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.

Assignment 3: Single-cell transcriptomics

• Hurdle
• Team or group-based
• Online

Mode

Written

Category

Computer Code, Paper/ Report/ Annotation, Practical/ Demonstration, Presentation, Tutorial/ Problem Set

Weight

20%

Due date

25/10/2024 2:00 pm

Other conditions

Student specific.

See the conditions definitions

Task description

Hurdle requirements

Submission guidelines

Online submission as instructed on assignment specification

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.

Final examination

• Hurdle
• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

40%

Due date

End of Semester Exam Period

2/11/2024 - 16/11/2024

Other conditions

Time limited.

See the conditions definitions

Task description

Hurdle requirements

Exam details

Submission guidelines

Deferral or extension

You may be able to defer this exam.

Course grading

Full criteria for each grade is available in the Assessment Procedure.

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 obtain an overall mark of 40% or more in the end of semester exam; and

3. You must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items and learning tasks; and

4. You must attend 100% of the laboratory component of the course ﾠand complete and submit ALL laboratory assessment.

The maximum grade you will receive will be a 2 if you:

1. Obtain an overall mark of 30% or less on the end of semester exam; and/or

2. Obtain a weighted average mark of 30% or less on the ﾠnon-examination course assessment items and learning tasks.

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.

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 SCIE3100/BINF7000 at learn.uq.edu.au

Please check the Announcements section of the Blackboard site regularly for information updates.

The course forum is also open for discussions on course related matters.

Learning activities

The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.

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.