Principles of Synthetic Biology (BIOT7050)

Course overview

This course will introduce the principles that underpin the development and implementation of synthetic biology approaches to address problems in industry, medicine, agriculture and other fields. We will explore how natural biological systems can be re-engineered by using biological molecules as ‘biobricks’ in modular arrangements of parts assembled into functional synbio ‘devices’ such as biocatalysts, novel metabolic pathways, genetic circuits, engineered organisms and DNA-scaffolded arrays. At the end of the course you will have a deep understanding of how the design-build-test-learn paradigm is used to develop innovative solutions to challenging global problems, such as in making processes environmentally friendly and sustainable, more effectively diagnosing and treating disease, enhancing food production and analysing and remediating pollution in the environment.

BIOT7050 is the defining course for the Field of Study in Synthetic Biology and Industrial Biotechnology.

The course will be presented in two parts. The first two thirds of the course comprises a set of lectures, workshops and other activities that will introduce the field of synthetic biology and its natural science and engineering basis, including exposing students to cutting-edge synthetic biology applications and their corresponding analysis and design tools. This will cover, but is not limited to the following topics:

1. Sourcing, design and engineering of biobricks for DNA, RNA and protein-based devices, that can be assembled to build synthetic biological systems;
2. Advanced techniques for engineering and assembly and automation of these methods in Biofoundries to enable massive refactoring of biological systems;
3. Techniques to visualise and quantify metabolic activities and efficiently control them to generate a specific output; and
4. Consideration of techno-economical, environmental and social and ethical aspects of engineered biological systems.

This section will feature a series of (guest) lectures from research leaders at UQ and beyond, all of whom are experts in different aspects of synthetic biology.

Having gained an understanding of contemporary means of manipulating biology for desired purposes in the first part of the course, students will then have the opportunity to demonstrate their creativity and ingenuity in preparing a research proposal on a freely-chosen synthetic biology-related topic in the second part of the course. This part of the course will scaffold the written assignment with workshops to develop specialised skills relevant to their assignments and the opportunity to obtain expert guidance on their proposal.

Course requirements

Assumed background

Students are assumed to have a background in (micro)biology, biotechnology or bioengineering and expected to have basic knowledge of molecular biology and biochemistry. Resources are provided for students lacking a background in these areas.

Jointly taught details

This course is jointly-taught with:

• Another instance of the same course

Lectures, workshops, and assessments are shared between the external and internal instance of BIOT7050.

Course contact

Course staff

Timetable

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

Additional timetable information

There are two weekly two-hour sessions for BIOT7050, which will each usually involve a one-hour lecture and an associated workshop or other activity. Some sessions towards the end of semester will be devoted to computer exercises and other activities designed to support the assignment.

Aims and outcomes

This course gives students of the life sciences and engineering the opportunity to develop a comprehensive understanding of synthetic biology and how it can be used to address global challenges such as climate change, diminishing natural resources and feeding a growing population. It focuses on introducing modern synthetic biology approaches and methods and will allow students to gain practical experience in using computer-based software and web-based tools for synthetic biology.

Following successful completion of the course, students will be able to integrate their background training in the natural sciences or engineering with their understanding of synthetic biology principles to propose synthetic biology approaches to address real-life applications in industrial biotechnology and chemistry, diagnosis and management of disease, agriculture and other fields.

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

Synbio Research Proposal - Oral Presentation

• Hurdle
• Identity Verified
• Online

Mode

Activity/ Performance, Oral

Category

Presentation

Weight

10%

Due date

21/10/2024 2:00 pm

Learning outcomes

L01, L08, L09, L10

Task description

Hurdle requirements

Submission guidelines

Submit your presentation slides 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.

Synbio Research Proposal - Written Report

• Hurdle

Mode

Written

Category

Paper/ Report/ Annotation, Project

Weight

40%

Due date

25/10/2024 2:00 pm

Learning outcomes

L01, L08, L09, L10

Task description

Hurdle requirements

Submission guidelines

Submit your project proposal 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.

End of Semester Exam

• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

50%

Due date

End of Semester Exam Period

2/11/2024 - 16/11/2024

Learning outcomes

L02, L03, L04, L05, L06, L07, L08, L09, L10

Task description

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 (presentation and research proposal).

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 non-examination course assessment items (presentation and research proposal).

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

Library resources are available on the UQ Library website.

Additional learning resources information

There are no required or recommended textbooks for this course. For students who want to refresh their knowledge in biochemistry and molecular biology, a list of references to textbooks and other material is available on UQ Blackboard.

Lecture slides and recordings will be made available before and shortly after the lecture, respectively. In addition, individual lecturers will recommend publications to support the content of their sessions.

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.