Molecular Systems Biology (BIOC3005)

Course overview

This course describes contemporary approaches to biological research, particularly the utility of large scale high-throughput technologies that are used in conjunction with cross-disciplinary & integrative methodologies in determining biological networks. Molecular systems biology is an integrative discipline that seeks to explain the properties & behaviour of complex biological systems in terms of their molecular components & their interactions.

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.

BIOC3005 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 analyse 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

BIOC3005 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 (e.g.ﾠ BIOC2000).

Prerequisites

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

[BIOC2000 or BIOC2900] AND [BIOL2202 or BIOL2902]

Jointly taught details

This course is jointly-taught with:

• BIOC7105

Lectures, practicals and, in some instances, assessment may be shared between BIOC3005 and BIOC7105.

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 for us to understand complex phenotypes at the organism level, and evolutionary dynamics at the population level.

New molecular technologies are enabling us to collect comprehensive data sets at the molecular systems level, and to gain new insights into the key regulatory mechanisms operating at the molecular systems level of biology. You will learn about the properties and behaviour of complex biological systems in terms of their molecular components and molecular interactions at the cellular and whole organism level. ﾠ

This course will provide excellent preparation for Honours research in genetics and molecular biology, biochemistry and microbiology. If you do not choose to do Honours, this course will provide you with insight into a systems paradigm for biological discovery that is relevant to all areas of biology. It will also provide you with experience in interpreting the literature in this field and presenting the information in oral and written form. With the advent of high-throughput molecular approaches such as genome sequencing, molecular systems biology is already starting to have a huge impact on all aspects of biological discovery and society.ﾠ

ﾠ

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

25/10/2024 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, L07

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 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.

Current topics in Genomics - discussion session

• Identity Verified
• In-person

Mode

Activity/ Performance, Oral

Category

Presentation

Weight

10%

Due date

2/09/2024 - 13/09/2024

Discussion sessions will take place during the wk7/8 'tutorial sessions'. Each student will only need to attend one session to which they have been allocated; details will be posted on Blackboard.

Other conditions

Student specific.

See the conditions definitions

Learning outcomes

L04, L05

Task description

Submission guidelines

This is an oral assessment item, so no submission is required. Students are required to attend the allocated contact hour for assessment.

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.

A note for approved extensions

Students with an approved extension must contact Dr Milos Tanurdzic (m.tanurdzic@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

26/08/2024 - 30/08/2024

16/09/2024 - 20/09/2024

21/10/2024 - 25/10/2024

Due dates: week 6, week 9 and week 13.

Monday practicals submit by 2 pm on the following Tuesday, Thursday practicals submit by 2 pm on the following Friday.

Learning outcomes

L03, L05, L08

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.

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.

Late Submission Notes

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

2/11/2024 - 16/11/2024

Learning outcomes

L01, L02, L04, 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

ﾠAssessment 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.ﾠ You must obtain an overall course mark of 50% or more; and

2. ﾠYou must obtain an overall mark of 40% or more on the end of semester exam; and

3. ﾠYou must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items (laboratory and presentation/discussion session) and learning tasks; and

4.ﾠ You must attend 100% of the laboratory components and complete and submit ALL laboratory assessment.

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

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

2.ﾠ Obtain a weighted average mark of 30% or less on the non-examination course assessment items (laboratory and presentation/discussion session) 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 andﾠ information about practicals/computer-based tutorials) may be found on the Blackboard site for BIOC3005 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.

Additional learning activity information

This is a computer-based practical

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.

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

• Laboratory Occupational Health and Safety