Molecular Systems Biology (BIOC7105)

Course overview

This course will explore contemporary approaches to understanding complex systems, such as cells or tissues, through studying molecular components and their interactions. We will cover ways to study cellular states using different -omics techniques, including how these large datasets can be analyzed and integrated to reveal details of the dynamics of whole cell processes. Molecular Systems Biology approaches are increasingly used in biotechnology and also form the basis for the generation of molecular models of cellular function.

Organisms are networks of interdependent molecular components working at all levels of living organisms such as cells, tissues and/or organisms. Life is organized into hierarchical, interdependent systems and new molecular technologies are enabling us to collect comprehensive data sets at the molecular level and gain insights into the key regulatory mechanisms acting at the molecular systems level of biology. This course will introduce you to the revolutionary field of molecular systems biology.

BIOC7105 provides theory and specialist knowledge of high-throughput technologies for uncovering biological networks. The course has a very strong technology element that will allow students to:

• Learn about modern, high-throughput molecular and genetic technologies/nanotechnologies that are revolutionizing biological research.

• Develop an understanding of the limitations of non-integrative approaches, and how a systems approach can complement the reductionist approach in biological research.

• Carry out a shotgun proteomics experiment that is part of a current research project, and use the data obtained to analyze the relationship between growth conditions and protein profiles obtained.

• Gain experience and competency in complex data analysis and the presentation of such data.

Course layout

BIOC7105 has three content modules and two practicals, introduced in the following order:

1) Proteomics & Protein-Protein Interactions

2) Comparative Genomics, Epigenomics and Transcriptomics

3) Metabolomics

Practicals:

1) Shotgun proteomics (weeks 1-9)

2) Quantitative Proteomics data analysis (weeks 11 & 12)

Course requirements

Assumed background

Participants in the course will benefit from some background in biochemistry equivalent to content taught to undergradudates in BIOC2000 or a good background in genetics and any type of systems level analyses.

Recommended prerequisites

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

BIOC7100

Incompatible

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

BIOC3005 (co-taught)

Course staff

Timetable

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

Additional timetable information

Please check your timetable online.

A lecture timetable with lecture titles will be available through Blackboard.

Aims and outcomes

This course will introduce you to molecular systems biology research. While an understanding of individual genes and proteins continues to be important, organisms are networks of interdependent components, and life is organized into hierarchical, interdependent systems. A systems approach is necessary to understand complex phenotypes at the organism level and evolutionary dynamics at the population level.

New molecular technologies are enabling collection of comprehensive data sets at the molecular systems level, generating new insights into the molecular function of complex biological systems such as cells, tissues and even whole organisms. You will learn about the properties and behaviour of these systems in terms of their molecular components and molecular interactions at the cellular and whole organism level. 

This course will provide excellent preparation for research in biotechnology, where molecular systems biology techniques are frequently used to evaluate production systems or to identify new targets for drug development and related applications. BIOC7105 is a practical intensive course, and you will get experience in generating and analyzing large-scale datasets, as well as identifying and discussing relevant literature.

Molecular systems biology is highly relevant to applied and discovery research and significantly impacts all aspects of biological discovery and society.

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

UQ Ripple

• Online

Mode

Written

Category

Product/ Design, Quiz, Reflection

Weight

10%

Due date

31/10/2025 2:00 pm

UQ Ripple will be used throughout the semester

Other conditions

Peer assessment factor.

See the conditions definitions

Learning outcomes

L01, L02, L06

Task description

Submission guidelines

This task will be completed in UQ Ripple throughout the semester. Completion of the tasks by the due date will be determined using the activity timestamps created by the UQ Ripple system.

Deferral or extension

You may be able to apply for an extension.

Applications for extension

Extension applications must be received no later than 24 hours after the published assessment due date and time.

Read the information contained in the following links carefully before submitting an application for extension to assessment due date.

For guidance on applying for an extension, information is available here.

For the policy relating to extensions, information is available here (Part D).

Information on medical certificates

Please note the University's requirements for medical certificates here.

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.

Journal Club

• Identity Verified
• In-person

Mode

Activity/ Performance, Oral

Category

Presentation

Weight

10%

Due date

25/08/2025 - 24/10/2025

Journal Clubs will take place during scheduled contact times. Each student will be required to present an analysis of one paper, attend all sessions for their journal club group and participate in discussions using a structured approach. Details will be available on Blackboard.

The number of sessions required for each journal club group will depend on the number of students in each group.

Other conditions

Student specific.

See the conditions definitions

Learning outcomes

L02, L03, L06

Task description

Submission guidelines

This is an oral assessment item, some documents may be needed to be submitted before the start of each session. Students are required to attend the allocated contact hour for assessment.

Deferral or extension

You may be able to apply for an extension.

The maximum extension allowed is 28 days. Extensions are given in multiples of 24 hours.

Applications for extension

Extension applications must be received no later than 24 hours after the published assessment due date and time.

Read the information contained in the following links carefully before submitting an application for extension to assessment due date.

For guidance on applying for an extension, information is available here.

For the policy relating to extensions, information is available here (Part D).

Information on medical certificates

Please note the University's requirements for medical certificates here.

A note for approved extensions

Students with an approved extension must contact Prof. Ulrike Kappler (u.kappler@uq.edu.au) to arrange an alternative time to complete the assessment.

Proteomics practical - laboratory notebook

• Hurdle
• In-person

Mode

Activity/ Performance

Category

Notebook/ Logbook, Practical/ Demonstration, Project, Reflection

Weight

40%

Due date

1/09/2025 - 5/09/2025

27/10/2025 - 31/10/2025

Due dates: ongoing for weekly ELN entries,

Week 6: submissions are due on Wednesday at 2 pm

In week 13, the Monday practical group will submit by 2 pm on the following Tuesday, the Thursday practical group will submit by 2 pm on the following Friday.

Learning outcomes

L04, L05, L06

Task description

Hurdle requirements

Submission guidelines

Electronic Lab Notebooks will be marked based on the entries in the electronic lab notebook used in the course. Timely submission will be judged using the entry's electronic timestamps.

The practical related assessment task will be submitted through Turnitin by a specific due date in week 6. Timely submission will be judged using the electronic timestamp of the submission.

Deferral or extension

You may be able to apply for an extension.

The maximum extension allowed is 28 days. Extensions are given in multiples of 24 hours.

Applications for extension

Extension applications must be received no later than 24 hours after the published assessment due date and time.

Read the information contained in the following links carefully before submitting an application for extension to assessment due date.

For guidance on applying for an extension, information is available here.

For the policy relating to extensions, information is available here (Part D).

Information on medical certificates

Please note the University's requirements for medical certificates here.

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 Examination

• Hurdle
• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

40%

Due date

End of Semester Exam Period

8/11/2025 - 22/11/2025

Learning outcomes

L01, L02, L03, L06

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 40% or more on the end of semester exam

2.       You must complete 100% of the laboratory/practical component of the course.

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 unonic media.

Students are encouraged to read the UQ Academic Integrity and Plagiarism

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

Blackboard

Additional material (including the Turnitin portal andﾠ information about practicals/computer-based tutorials) may be found on the Blackboard site for BIOC3005/7105 at learn.uq.edu.au

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

Recommended Reading

Omics Approaches Technologies and applications, 2018, Springer. (book)

Editors: Preeti Arivaradarajan, Gauri Misra.

This text provides a general introduction to -omics techniques that form the basis of systems biology.

https://doi.org/10.1007/978-981-13-2925-8

 https://doi.org/10.1007/978-981-13-2925-8

Bioanalytics: Analytical Methods and Concepts in Biochemistry and Molecular Biology

Friedrich Lottspeich (Editor), Joachim W. Engels (Editor)

ISBN: 978-3-527-33919-8 March 2018 1134 Pages

This book may be used to support learning, but it is not mandatory.

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 for Students Policy and Procedure

Learn more about UQ policies on my.UQ and the Policy and Procedure Library.

You'll also need to be aware of the following policies and procedures while completing this course:

• Laboratory Occupational Health and Safety