Since its much heralded inception in the early 2000’s, Synthetic Biology (SynBio) has gained significant attention and sizeable funding from public and private sectors around the world. From its emergence as a boldly stated intention to engineer biology, through to an increasingly mature and diverse discipline, the field continues to promise solutions to the global challenges we face today. It is becoming increasingly possible to engineer living cells in the same way as digital technology, complete with dedicated program languages and assembly tools to quickly and modularly combine biological “parts” for a tailored purpose. Proponents promise clean energy, sustainable biomanufacturing, food security and effective disease intervention that will transform our society, alter the way we interact with our environment, and allow us to sustainably provide goods and services across all economic sectors.

 

This course will form the basis of the ANU entry into the Australian SynBio Challenge, launched in 2020 to contribute to a vision of a strong, innovative and responsible Synthetic Biology sector in Australia. Students will be expected to work cohesively in a team, designing, building and testing a synthetic biology solution to a significant problem. Students will be expected to learn about Synthetic Biology and its potential applications in the process, with a particular emphasis on developing entrepreneurial skills and knowledge of the commercialisation process. The course will be framed by two main events, a “design review” and a “final showcase”, at the start and end of the semester, that aim to bring students, academics and industry together to realise visions for a sustainable future.

 

This is an Honours Pathway Course.

Learning Outcomes

Upon successful completion, students will have the knowledge and skills to:

1. Explain fundamental principles of Synthetic Biology, including modularity and abstraction.
2. Critically analyse published Synthetic Biology literature to identify strategies leading to the design of an innovative solution to a significant environmental, industrial or medical problem.
3. Apply experimental techniques and relevant software to Synthetic Biology.
4. Demonstrate ability to apply different writing styles for different purposes, such as how grant proposals differ from research reports and journal articles.
5. Discuss and reflect on the ethical and social implications of their project.
6. Demonstrate knowledge of commercialisation pathways between industry and university research.
7. Collaborate in a multidisciplinary team to meet the design challenge.

Research-Led Teaching

This is primarily a research led course, in which you will work collaboratively in a team of approximately 10 students to independently design and build a synthetic biology concept with appropriate mentoring from academics and the local Synthetic Biology community via participation in the Australasian Synthetic Biology Challenge (https://www.aussynbiochallenge.org/). The team will have a cash budget and scientific resources available from our industrial sponsors (such as DNA synthesis) in order to achieve their objectives.

Field Trips

BIOL3188 would normally include travel to attend the Final showcase, but this year it is being held at ANU!

Additional Course Costs

The 2023 ANU team has a small cash budget provided by Dr Burgio/JCSMR to cover any expenses not covered by the in-kind contributions of the Challenge industrial sponsors.

Examination Material or equipment

All assessment will be open book.

Required Resources

Safety glasses and enclosed shoes are required for any lab work.

Recommended Resources

Recommended student system requirements 

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

• video material, similar to YouTube, for lectures and other instruction
• two-way video conferencing for interactive learning
• email and other messaging tools for communication
• interactive web apps for formative and collaborative activities
• print and photo/scan for handwritten work
• home-based assessment.

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.
• Webcam
• Speakers and a microphone (e.g. headset)
• Reliable, stable internet connection. Broadband recommended. If using a mobile network or wi-fi then check performance is adequate.
• Suitable location with minimal interruptions and adequate privacy for classes and assessments.
• Printing, and photo/scanning equipment

For more information please see https://www.anu.edu.au/students/systems/recommended-student-system-requirements

Staff Feedback

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

• written comments
• verbal comments
• feedback to whole class, groups, individuals, focus group etc

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). Feedback can also be provided to Course Conveners and teachers via the Student Experience of Learning & Teaching (SELT) feedback program. SELT surveys are confidential and also provide the Colleges and ANU Executive with opportunities to recognise excellent teaching, and opportunities for improvement.

Class Schedule

Week/Session	Summary of Activities	Assessment
1	The Aus SynBio Challenge encourages teams to adhere to the Design-Build-Test-Learn (DBTL) paradigm by structuring the challenge around four main phases. The teams will be loosely synchronised as they move through the phases of the cycle, coinciding with two major events, the Design Review and Final Showcase. Due to the annual timetable of the challenge not corresponding to the duration of a single course, the Design Phase and Design Review will be conducted on a volunteer basis during the 1st semester. The proposed structure will look like as follows: a. Design phase - In the first phase, Teams will be asked to select their Challenge topic and develop possible prototype solutions through genetic design. It is intended this phase of the competition will be aided by a series of seminars with mentors that have extensive knowledge of engineering design approaches, genetic design frameworks and the software tools available. These resources will be provided by the challenge organisers. b. Design Review - Designs will be critiqued by an expert panel, concluding in direct feedback at a virtual workshop at the end of semester 1. c. Build phase - following the review, teams will be asked to submit genetic sequences for DNA synthesis at the start of semester 2. Teams will spend the next few weeks assembling their constructs (e.g., plasmids, strains, cellular consortia). They will be provided with resources that will help them with their assembly strategies (enzymes, purification columns) by industrial sponsors and under supervision from experienced mentors from ANU faculty.	Before the mid-semester break (4th - 17th of September, 2023) students will receive feedback from their skill development assignment. This will be in the form an online assessment of ability to use online synthetic biology software to design a genetic assembly. (Assessment Task 2)
2	d. Test phase - A significant focus of the competition will be placed in experimental testing and characterisation of their genetic designs and prototype solutions. Teams will test their constructs using analytical equipment provided by their institution. They will be coached on how to obtain reliable and reproducible results so that they can be compared with other teams and the literature, while being encouraged to develop and follow Challenge-wide standards for part characterisation. e. Learn phase - Teams will be expected to assess their results in the context of their original proposed design. They will preview and present the project outcomes at anational showcase event.	The Final Showcase is the main event of the Australasian SynBio Challenge (https://www.aussynbiochallenge.org/) associated with this course. Participation in preparing the teams' presentation, and attendance (currently via video link due to COVID restrictions) at the event is mandatory (Assessment Task 3) unless an exemption has been granted by the course convenor (requires evidence of a timetable clash with compulsory practical or exam for another ANU course, medical certificate, etc). The final showcase is scheduled for October, precise dates TBA.
3	Grant proposal assessment	If you were to continue your project in the following year in order to obtain more preliminary results and develop its commercialisation potential, what extra experiments / tests would you perform, and what resources and equipment would you need to achieve this? Your assessment is to write a convincing grant proposal in order to obtain the necessary funding from a prospective funding body (Assessment Task 1).The proposal should be no more than ten double-spaced pages in 12 point Times. Figure and table captions should be single-spaced in 12 point Times. The 10-page limit includes all text, figures and tables but excludes the reference list, research timetable and budget table. Numbered or non-numbered citation styles may be used.

Tutorial Registration

Timing of tutorials prior to the opening of the Skill development and Grant proposal assessments will be organised via an online poll with the class and advertised on wattle. Attendance will not be compulsory but strongly encouraged.

Assessment Summary

Assessment task	Value	Due Date	Return of assessment	Learning Outcomes
Grant proposal	80 %	27/10/2023	10/11/2023	1,2,3,4,5,6
Skill development assignment	20 %	25/08/2023	01/09/2023	1,2,3,7
Contribution to Final Showcase	0 %	29/09/2023	29/09/2023	1,2,3,4,5,6,7

* 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 Integrity Rule before the commencement of their course. Other key policies and guidelines include:

• Academic Integrity Policy and Procedure
• Student Assessment (Coursework) Policy and Procedure
• Extenuating Circumstances Application
• Student Surveys and Evaluations
• Deferred Examinations
• Student Complaint Resolution Policy and Procedure
• Code of practice for teaching and learning

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 Academic Skills website. In rare cases where online submission using Turnitin software is not technically possible; or where not using Turnitin software has been justified by the Course Convener and approved by the Associate Dean (Education) on the basis of the teaching model being employed; students shall submit assessment online via ‘Wattle’ outside of Turnitin, or failing that in hard copy, or through a combination of submission methods as approved by the Associate Dean (Education). The submission method is detailed below.

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

BIOL3188 seeks to be an inclusive course. Juliey Beckman (Juliey.Beckman@anu.edu.au) is the Science, Health & Medicine Disability contact. She can provide advice and assistance to students with a disability, particularly with respect to selecting courses, suggesting possible adjustments and helping students discuss adjustments with course conveners. Students with a disability (including illness, mental health) can also register with Access & Inclusion to receive assistance.

Examination(s)

There is no exam for this course.

Assessment Task 1

Grant proposal

If you were to continue your project in the following year in order to obtain more preliminary results and develop its commercialisation potential, what extra experiments / tests would you perform, and what resources and equipment would you need to achieve this? Your assessment is to write a convincing grant proposal in order to obtain the necessary funding from a prospective funding body.

The proposal should be no more than ten double-spaced pages in 12 point Times. Figure and table captions should be single-spaced in 12 point Times. The 10-page limit includes all text, figures and tables but excludes the reference list, research timetable and budget table. Numbered or non-numbered citation styles may be used.

Assessment Task 2

Skill development assignment

The ANU team uses the online software tool Benchling to design their biological devices and keep an accurate record of results. This assignment will test your ability to utilise the full functionality of this software (for e.g, creating a golden assembly or design gRNA for CRISPR editing).

Assessment Task 3

Contribution to Final Showcase

The Final Showcase is the main event of the Australasian SynBio Challenge (https://www.aussynbiochallenge.org/) associated with this course. Participation in preparing the teams' presentation, and attendance at the event is mandatory unless an exemption has been granted by the course convenor (requires evidence of a timetable clash with compulsory practical or exam for another ANU course, medical certificate, etc). Final showcase with be on the October the 29th, hosted at the ANU Physics auditorium, for the whole day.

Academic Integrity

Academic integrity is a core part of the ANU culture as a community of scholars. The University’s students are an integral part of that community. The academic integrity principle commits all students to engage in academic work in ways that are consistent with, and actively support, academic integrity, and to uphold this commitment by behaving honestly, responsibly and ethically, and with respect and fairness, in scholarly practice.

The University expects all staff and students to be familiar with the academic integrity principle, the Academic Integrity Rule 2021, the Policy: Student Academic Integrity and Procedure: Student Academic Integrity, and to uphold high standards of academic integrity to ensure the quality and value of our qualifications.

The Academic Integrity Rule 2021 is a legal document that the University uses to promote academic integrity, and manage breaches of the academic integrity principle. The Policy and Procedure support the Rule by outlining overarching principles, responsibilities and processes. The Academic Integrity Rule 2021 commences on 1 December 2021 and applies to courses commencing on or after that date, as well as to research conduct occurring on or after that date. Prior to this, the Academic Misconduct Rule 2015 applies.

 

The University commits to assisting all students to understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. All coursework students must complete the online Academic Integrity Module (Epigeum), and Higher Degree Research (HDR) students are required to complete research integrity training. The Academic Integrity website provides information about services available to assist students with their assignments, examinations and other learning activities, as well as understanding and upholding academic integrity.

Online Submission

You will be required to electronically sign a declaration as part of the submission of your assignment. Please keep a copy of the assignment for your records. Unless an exemption has been approved by the Associate Dean (Education) submission must be through Turnitin.

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

Individual assessment tasks may or may not allow for late submission. Policy regarding late submission is detailed below:

• Late submission not permitted. If submission of assessment tasks without an extension after the due date is not permitted, a mark of 0 will be awarded. This applies for skill development Assessment Task 2.
• Late submission permitted. 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. This applies for grant proposal Assessment Task 1.

Referencing Requirements

The Academic Skills website has information to assist you with your writing and assessments. The website includes information about Academic Integrity including referencing requirements for different disciplines. There is also information on Plagiarism and different ways to use source material.

Returning Assignments

All assessment must be submitted via email to the course convenor (joseph.brock@anu.edu.au).

Extensions and Penalties

Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure. Extensions may be granted 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

No

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 Access 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 all ANU students