LQB583 Molecular Systems Biology

Unit Outline: Semester 1 2024, Gardens Point, Internal

Overview

Over the past decade, technological advances have transformed research capabilities to the point where multiple biomolecular targets, such as genes, proteins or metabolites, within a single system can be investigated simultaneously. Systems biology involves the study of a complex system through multiple biomolecular perspectives to determine molecular relationships and functions across a biological system of interest. Resulting data is often interrogated using advanced bioinformatics to determine how networks of molecules relate to specific phenotypes. Importantly, such approaches are becoming increasingly prevalent in the laboratories of most leading research institutions globally. Thus, the skills necessary to extract meaningful biological information using omics approaches are highly sought after. This unit will provide you with a strong overview of various omics approaches and expose you to advanced bioinformatics tools for solving complex biological problems.

Learning Outcomes

On successful completion of this unit you will be able to:

1. Justify your understanding of the different technologies used in 'omics' fields.
2. Exemplify practical capability in wet-lab and bioinformatic approaches in the analysis of basic 'omics' datasets.
3. Communicate, by written means, a capacity to analyse, interpret and critically evaluate strategies for investigating functional relationships of 'omics' data and approaches.

Content

Learning Approaches

This unit uses blended learning approaches. Theoretical aspects are provided by a range of online resources developed specifically for the unit and/or traditional face-to-face lectures. Lectures are coupled with a series of practicals and workshops that illustrate the technologies presented in the lecture material and encourage development of strategic, critical and systems based thinking. The various components of this unit are designed to produce learning outcomes that enhance your appreciation and comprehension of the global systems biology revolution. The unit is designed to produce learning outcomes that go beyond the traditional approach of knowledge transfer and acquisition. There is a greater emphasis on concepts and interpretation of information than in the traditional didactic lecture format and the unit is designed to provide opportunities for deeper learning outcomes beyond simple knowledge or concept acquisition. In particular, hands-on practicals, workshops and assignments are designed to encourage a capacity for independent and critical thinking, literature research and information management skills, written and oral communication skills, hypothesis generation and testing, lateral thinking and problem solving skills, and sustainable individual and group learning strategies and habits. Students will experience having to use and engage with multiple 'omics discipline areas to explore data and complex biomedical problems.

Feedback on Learning and Assessment

Feedback will be available via your unit coordinator in verbal meetings if specifically requested. Formative feedback will be provided via contact with the teaching team at the scheduled learning activities. Class feedback on summative pieces will be provided in lectures and/or in writing on the Canvas site once all assessment items have been graded.

Assessment

Overview

All assessment will be graded as a percentage of the total assessment contribution to the unit based on assessment criteria that will be provided for each item. The assessments for the unit are staggered throughout the semester as described in detail below and are completed independently by each individual in the unit. Progressive discussion including formative feedback will be available to students who actively participate in the scheduled learning activities for these tasks during those learning activities.

Unit Grading Scheme

7- point scale

Assessment Tasks

Assessment: Laboratory/Practical

You will undertake the role of a senior research scientist within an omics-research laboratory, where you will critically review and respond to a failed experimental approach provided by a distressed colleague via an email correspondence. Applying your understanding of omics methodologies acquired in laboratory practice and through independent research, you will provide an email response to your colleague detailing the specific issues and recommendations to address the failed endeavour.

This assessment is eligible for the 48-hour late submission and assignment extensions.

Assessment: Bioinformatic Workshops

As a bioinformatician, you will be required at times to simultaneously work for different clients to address their project needs. As a new bioinformatician based at a specialist organisation, you will undertake the bioinformatic and statistical analyses of four datasets from four different omics fields, providing a critical analysis and interpretation of results. You will be required to complete your responses within a template document to be submitted to the senior bioinformatician for review before they are released to the client.

You will be required to undertake four independent self-directed learning bioinformatics modules applied to four different 'omics' areas. Based on the content covered in lectures and workshops.

This assessment is eligible for the 48-hour late submission and assignment extensions.

Assessment: Essay

As a graduate scientist, you will be required to produce either (i) an internal research grant-style project proposal, which details a methodological pipeline of multi-omics tools and approaches to solve a complex biological problem, to be submitted to your superiors for funding your ongoing research, or (ii) an informative literature review of the relevant omics approaches and tools used to investigate a significant human health and disease issue, to be submitted to your clinical collaborator to assist with their understanding of omics applications within their field. Through either approach, you will be exposed to authentic omics methods and tools and demonstrate your understanding of these through critical explanation and application in real-world contextual settings.

This assessment has two summative sub-components due around week 4 (draft topic selection) and week 6-7 (draft essay structure) of semester that are designed to help you structure and plan out your essay document.

This assessment is eligible for the 48-hour late submission and assignment extensions.

Academic Integrity

Students are expected to engage in learning and assessment at QUT with honesty, transparency and fairness. Maintaining academic integrity means upholding these principles and demonstrating valuable professional capabilities based on ethical foundations.

Failure to maintain academic integrity can take many forms. It includes cheating in examinations, plagiarism, self-plagiarism, collusion, and submitting an assessment item completed by another person (e.g. contract cheating). It can also include providing your assessment to another entity, such as to a person or website.

You are encouraged to make use of QUT’s learning support services, resources and tools to assure the academic integrity of your assessment. This includes the use of text matching software that may be available to assist with self-assessing your academic integrity as part of the assessment submission process.

Further details of QUT’s approach to academic integrity are outlined in the Academic integrity policy and the Student Code of Conduct. Breaching QUT’s Academic integrity policy is regarded as student misconduct and can lead to the imposition of penalties ranging from a grade reduction to exclusion from QUT.

Requirements to Study

Costs

Cost of lab gowns and safety protection glasses are the students responsibility.

Resources

Resource Materials

Safety and protective equipment

Practicals will require personal protective equipment supplied by each student:

1. Laboratory Gown - Rear fastening 100% cotton or polyester/cotton mix
2. Safety eye protection glasses - selected and used in accordance with Australian Safety Standards
3. Fully enclosed non-slip shoes

Risk Assessment Statement

This unit includes a laboratory component. In order that you become proficient in necessary practical skills, you will be trained in the handling of equipment, materials and specimens normally associated with this discipline. You are required to view a Health & Safety Induction video and complete an online health and safety quiz prior to being permitted into the laboratory, to access please follow this link Health & Safety Induction. A passing score of 10/10 is required and will be checked prior to entry to the first laboratory session. You may repeat the quiz until this score is achieved. You are also referred to the Faculty of Health's Health & Safety Web Site for further information.

If you have an underlying health condition you are encouraged to consult the lecturer in charge of the unit, as you may be required to take additional precautions on occasions.

Course Learning Outcomes

LS40 Bachelor of Biomedical Science

1. Critically review, analyse and synthesise foundational knowledge in a broad range of biomedical discipline areas and in depth theoretical, technical and practical knowledge in specialised discipline areas.
   Relates to: Laboratory/Practical, Bioinformatic Workshops, Essay
2. Demonstrate the technical skills required to solve multi-disciplinary problems in biomedical research, industry and clinical settings and do so in an ethical, safe and responsible manner.
   Relates to: Laboratory/Practical, Bioinformatic Workshops
3. Demonstrate the cognitive skills required to find solutions to scientific problems.
   Relates to: Laboratory/Practical, Bioinformatic Workshops, Essay
4. Apply knowledge and skills to rapidly source, critically analyse and communicate biomedical science information using appropriate technologies.
   Relates to: Essay