Unit convenor and teaching staff |
Unit convenor and teaching staff
Lecturer
Martin Ostrowski
Contact via 02 9850 6273
4WW 336
by appointment
Lecturer
Matthew McKay
Robert Willows
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Credit points |
Credit points
4
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Prerequisites |
Prerequisites
Admission to MRes
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Corequisites |
Corequisites
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Co-badged status |
Co-badged status
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Unit description |
Unit description
This unit addresses some advanced methods of analysis utilised in the biomolecular sciences. Biomolecular sciences spans the study of individual molecular structures and biochemical reactions to also encompass the 'omics' sciences of genomics, proteomics, metabolomics and glycomics. These sciences all generate large and complex datasets that require specialized software and methods to assemble and analyse. The analyses are challenging, as they not only require a good knowledge of biochemistry, molecular biology, and cell and developmental biology, but also an understanding of limitations of both the software and the data quality. This unit will provided a background to the data acquisition methods, quality control of the datasets, and analysis methods within a number of these areas. Most importantly it will provide hands-on experience in the analysis of real large-scale datasets and the correct use of appropriate analysis tools.
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Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
On successful completion of this unit, you will be able to:
Name | Weighting | Hurdle | Due |
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Take home examination | 10% | No | 25th August |
Proteomics Data AnalysisReport | 25% | No | 6th October |
Genomics quiz | 10% | No | 12th October |
Genomics Data Presentation | 25% | No | 2rd November |
Final Examination | 30% | No | Examination Period |
Due: 25th August
Weighting: 10%
Exam assessing some of the fundamental principles and concepts important in the application of protein mass spectrometry and proteomics, including peptide fragmentation, targeted mass spectrometry and principles of experimental design Content from Week 1-3 will be assessed in the form of short answer questions. There will be 5 questions of equal weighting.
Due: 6th October
Weighting: 25%
Students will be given a dataset containing information from a large scale quantitation LC/MS experiment. The dataset needs to be evaluated using Perseus, and a report containing information about quantitative changes presented. The report should present visual statistical analysis providing an overview of the experiment and illustrating differences in samples (e.g. Hierarchical Clustering, Principle-Component-Analysis), and an evaluation of key proteins and the pathways they are associated with. The report should contain sufficient methodological detail appropriate for publication purposes in quality proteomics journals.
Due: 12th October
Weighting: 10%
Students will be given raw paired-end next generation sequencing data equivalent to a complete bacterial genome. Students will be tasked with assembling the data following the necessary pre-processing steps, and then annotating the genes and features on the assembled DNA using tools covered in the preceding sessions. The task will be assessed by 1. producing a fasta file of assembled dna contigs, 2. a file of gene/ORF annotations, 3. filling in the summary table (provided) and answering 3 short questions about their data.
Due: 2rd November
Weighting: 25%
Students to be given raw next generation sequencing reads from an unknown dataset. These are to be analysed following guidelines presented in the tutorials. The outcomes of these results are to be given as an Oral Presentation of 12min plus 3min question time.
Due: Examination Period
Weighting: 30%
This will be a 2h exam consisting of a series of problem solving, data interpretation questions and short essays.
This unit uses team-based teaching in the form of 'lectorials' that encompass both lectures and hands-on experiences in using various data analysis software programs and tools. The tutors are actively involved in research activities to bring knowledge from real-world experiences in their respective fields. All class sessions take place on Friday 9am-1pm in F7B433 unless otherwise instructed. Tutorials will NOT be recorded. You must attend these tutorials to gain practical experience with data analysis. As some of the assessment is based on your practical use of specific software it is essential that you attend these classes.
It is expected that each student will bring to class a laptop PC computer to install data analysis software, or prior arrangements must be made with the convenor.
Software Requirements
Proteomics software used in this module can be installed in weeks 1 or 2 and will be available for use during the software sessions starting week 3.
Genomics, data analysis and programming software used in this module can either be installed onto the students laptop or will be made available via access to a university Linux server. Local installation of up-to-date versions of the following software will be required.
All official correspondence with lecturers and tutors is to be made using the CBMS793 iLearn website.
Week |
Date |
Title |
Lecturer |
Proteomics |
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1 |
3 Aug |
Unit overview
Introduction to protein mass spectrometry (detecting ions - instruments, scan types, peptide fragmentation and common proteomic workflows) - Introduction to quantitative mass spectrometry techniques |
MO
MMcKay |
2 |
10 Aug |
Principles of protein identification: peptide fragmentation and the automation of spectral assignment - Targeted Mass Spectrometry (From SRM to DIA: Using Area Under the Curve (AUC) approaches for quantitation via SWATH) |
MMcKay |
3 |
17 Aug |
Principles of experiment design and statistical analysis in proteomics Quantitation of Large DIA Proteomic Datasets |
MMcKay
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4 |
24 Aug |
Tools for the quantitation of peptides and proteins PeakView and Perseus |
MMcKay
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5 |
31 Aug |
Combining experimental design with statistical power in DIA experiments
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McKay |
6 |
7 Sept |
DIA data analysis |
McKay |
7 |
14 Sept |
Pathway mapping and data mining |
McKay |
Mid-Semester Break 17 Sept-2 Oct |
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Core skills for 'Omics |
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8 |
5 Oct |
Genomics Introduction
Introduction to the shell and useful tools |
IP, MO |
9 |
12 Oct |
Introduction to sequencing data quality control, assembly and annotation
Genomics Quiz |
MO |
10 |
19 Oct |
Metagenomic analysis 1
Introduction to R |
MO |
11 |
26 Oct |
Metagenomic analysis 2
Transcriptome analysis tools |
MO |
12 |
2 Nov |
Genomics - Oral Presentations |
MO |
13 |
9 Nov |
Revision |
McKay MO |
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No changes from the unit offered in S2, 2016