Bioinformatics

Bioinformatics

BIOL3018 Gene Technology and Genomics

Credit points: 6 Teacher/Coordinator: A/Prof Neville Firth Session: Semester 1 Classes: Two 1-hour lectures and one 3-hour practical per week. Prerequisites: (MBLG2072 or MBLG2972) and 6cp from either (MBLG2071 or MBLG2971) or Intermediate BIOL. Prohibitions: BIOL3918 Assessment: One 2-hour exam (60%), assignments (40%). Mode of delivery: Normal (lecture/lab/tutorial) day
A unit of study with lectures, practicals and tutorials on the application of recombinant DNA technology and the genetic manipulation of prokaryotic and eukaryotic organisms. Lectures cover the applications of molecular genetics in biotechnology and consider the regulation, impact and implications of genetic engineering and genomics. Topics include biological sequence data and databases, comparative genomics, the cloning and expression of foreign genes in bacteria, yeast, animal and plant cells, novel human and animal therapeutics and vaccines, new diagnostic techniques for human and veterinary disease, and the genetic engineering of animals and plants. Practical work may include nucleic acid isolation and manipulation, gene cloning and PCR amplification, DNA sequencing and bioinformatics, immunological detection of proteins, and the genetic transformation and assay of plants.
BIOL3918 Gene Technology and Genomics Advanced

Credit points: 6 Teacher/Coordinator: A/Prof Neville Firth Session: Semester 1 Classes: Two 1-hour lectures and one 3-hour practical per week. Prerequisites: Distinction average across (MBLG2072 or MBLG2972) and 6cp from either (MBLG2071 or MBLG2971) or Intermediate BIOL. Prohibitions: BIOL3018 Assessment: One 2-hour exam (60%), assignments (40%). Mode of delivery: Normal (lecture/lab/tutorial) day
Qualified students will participate in alternative components of BIOL3018 Gene Technology & Genomics. The content and nature of these components may vary from year to year.
BIOL3026 Developmental Genetics

Credit points: 6 Teacher/Coordinator: A/Prof Mary Byrne Session: Semester 2 Classes: Twenty-four 1 hour lectures/tutorials per semester and up to 3 hours laboratory per week. Prerequisites: (MBLG2072 or MBLG2972) and 6cp from either (MBLG2071 or MBLG2971) or Intermediate BIOL. Prohibitions: BIOL3926, BIOL3929 Assessment: One 2-hour exam, assignments (100%). Mode of delivery: Normal (lecture/lab/tutorial) day
Developmental genetics discusses major concepts and our current understanding of developmental biology with an emphasis on molecular genetics. The developmental genetics of animal and plant systems will be investigated, along with approaches used to determine gene function in relation to development of complex multicellular organisms. Topics include the features and resources for model organisms; the generation of mutants for forward and reverse genetics; the application of mutants to the study gene function and gene networks; spatial and temporal gene expression in pattern formation; quantitative trait loci analysis; utility of genome wide association studies; epigenetics in relation to inheritance; genome information in the study of human genetics. Reference will be made to the use of modern techniques in developmental biology such as transgenics, recombinant DNA technology, tissue-specific expression analysis. Various methods of genetic mapping will be covered. Practical work complements the theoretical aspects of the course and develops important skills in genetics.
BIOL3926 Developmental Genetics (Advanced)

Credit points: 6 Teacher/Coordinator: A/Prof Mary Byrne Session: Semester 2 Classes: Twenty-four 1 hour lectures/tutorials per semester and up to 3 hours laboratory per week. Prerequisites: Distinction average across (MBLG2072 or MBLG2972) and 6cp from either (MBLG2071 or MBLG2971) or Intermediate BIOL. Prohibitions: BIOL3929, BIOL3026 Assessment: One 2-hour exam, assignments (100%). Mode of delivery: Normal (lecture/lab/tutorial) day
Qualified students will participate in alternative components to BIOL3026 Developmental Genetics. The content and nature of these components may vary from year to year. Some assessment will be in an alternative format to components of BIOL3026.
BIOL3044 Evolution and Biodiversity

Credit points: 6 Teacher/Coordinator: A/Prof M. Henwood Session: Semester 1 Classes: Two lectures and three practicals per week. Prerequisites: 12 credit points of Intermediate BIOL; or 6 credit points of Intermediate BIOL and (MBLG2072 or MBLG2972). Prohibitions: PLNT3903, PLNT3003, BIOL3025, BIOL3944, BIOL3925 Assessment: Practical reports and/or presentations (60%), one 1.5-hour exam (40%). Mode of delivery: Normal (lecture/lab/tutorial) day
How did the diversity of life arise? Why are there so many species? Why do animals and plants seem so well designed for their environments? How do we explain patterns of distribution across continents? These are some of the key questions that we will examine in this Unit. The Unit begins with a survey of the history of evolutionary thought, and the so-called 'new synthesis'; the melding of Darwinian evolution, systematics and genetics. The Unit will provide training in the principles, methods, and applications of evolutionary biology including systems of classification, the genetics of speciation and hybrid zones, molecular evolution, reconstruction of phylogenies, population genetics, historical interpretation of geographic distributions, evolution of sex, adaptation, human evolution, and selfish gene theory. Examples from a broad range of organisms and data sources will be used throughout the Unit. This Unit is valuable for students who intend to seek employment in areas such as biodiversity research, bioinformatics, ecology, taxonomy, biological conservation and teaching.
Textbooks
Freeman and Herron (2011) Evolutionary Analysis, Pearson/Prentice Hall
BIOL3944 Evolution and Biodiversity (Advanced)

Credit points: 6 Teacher/Coordinator: A/Prof Murray Henwood Session: Semester 1 Classes: Two lectures or three practicals per week. Prerequisites: Distinction average across either 12 credit points of Intermediate BIOL, or 6 credit points of Intermediate BIOL and (MBLG2072 or MBLG2972). Prohibitions: PLNT3003, BIOL3044, BIOL3925, BIOL3025, PLNT3903 Assessment: Practical reports and/or presentations (60%), one 1.5-hour exam (40%). Mode of delivery: Normal (lecture/lab/tutorial) day
The content will be based on the standard unit BIOL3044 but qualified students will participate in alternative components at a more advanced level. How did the diversity of life arise? Why are there so many species? Why do animals and plants seem so well designed for their environments? How do we explain patterns of distribution across continents? These are some of the key questions that we will examine in this Unit. The Unit begins with a survey of the history of evolutionary thought, and the so-called 'new synthesis'; the melding of Darwinian evolution, systematics and genetics. The Unit will provide training in the principles, methods, and applications of evolutionary biology including systems of classification, the genetics of speciation and hybrid zones, molecular evolution, reconstruction of phylogenies, population genetics, historical interpretation of geographic distributions, evolution of sex, adaptation, human evolution, and selfish gene theory. Examples from a broad range of organisms and data sources will be used throughout the Unit. This Unit is valuable for students who intend to seek employment in areas such as biodiversity research, bioinformatics, ecology, taxonomy, biological conservation and teaching.
Textbooks
Freeman and Herron (2011) Evolutionary Analysis, Pearson/Prentice Hall
BCHM3092 Proteomics and Functional Genomics

Credit points: 6 Teacher/Coordinator: A/Prof Stuart Cordwell, Jill Johnston Session: Semester 2 Classes: Two 1-hour lectures per week and one 3-hour practical per week. Prerequisites: (MBLG1001/1901) and 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971 or BCHM2072/2972). For BMedSc: (18 credit points of BMED including BMED2401 and BMED2405 and one of MBLG2071/2971 or BCHM2071/2971) or (BMED2801 and BMED2802 and BMED2804). Prohibitions: BCHM3992, BCHM3098 Assessment: One 2.5-hour exam, practical work (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit of study will focus on the high throughput methods for the analysis of gene structure and function (genomics) and the analysis of proteins (proteomics), which are at the forefront of discovery in the biomedical sciences. The course will concentrate on the hierarchy of gene-protein-structure-function through an examination of modern technologies built on the concepts of genomics versus molecular biology, and proteomics versus biochemistry. Technologies to be examined include DNA sequencing, nucleic acid and protein microarrays, two-dimensional gel electrophoresis of proteins, uses of mass spectrometry for high throughput protein identification, isotope tagging for quantitative proteomics, high-performance liquid chromatography, high-throughput functional assays, affinity chromatography and modern methods for database analysis. Particular emphasis will be placed on how these technologies can provide insight into the molecular basis of changes in cellular function under both physiological and pathological conditions as well as how they can be applied to biotechnology for the discovery of biomarkers, diagnostics, and therapeutics. The practical component is designed to complement the lecture course and will provide students with experience in a wide range of techniques used in proteomics and genomics.
Textbooks
Kraj A and Silberring J Proteomics Introduction to Methods and Applications Wiley 2008
BCHM3992 Proteomics and Functional Genomics (Adv)

Credit points: 6 Teacher/Coordinator: A/Prof Stuart Cordwell, Jill Johnston Session: Semester 2 Classes: Two 1-hour lectures per week and one 3-hour practical per fortnight. Prerequisites: (MBLG1001/1901) and Distinction in 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971 or BCHM2072/2972). For BMedSc: (18 credit points of BMED including BMED2401 and Distinction in BMED2405 and one of MBLG2071/2971 or BCHM2071/2971) or (Distinction average in BMED2801 and BMED2802 and BMED2804). Prohibitions: BCHM3092, BCHM3098 Assessment: One 2.5-hour exam, practical work (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit of study will focus on the high throughput methods for the analysis of gene structure and function (genomics) and the analysis of proteins (proteomics) which are at the forefront of discovery in the biomedical sciences. The course will concentrate on the hierarchy of gene-protein-structure-function through an examination of modern technologies built on the concepts of genomics versus molecular biology, and proteomics versus biochemistry. Technologies to be examined include DNA sequencing, nucleic acid and protein microarrays, two-dimensional gel electrophoresis of proteins, uses of mass spectrometry for high throughput protein identification, isotope tagging for quantitative proteomics, high-performance liquid chromatography, high-throughput functional assays, affinity chromatography and modern methods for database analysis. Particular emphasis will be placed on how these technologies can provide insight into the molecular basis of changes in cellular function under both physiological and pathological conditions as well as how they can be applied to biotechnology for the discovery of biomarkers, diagnostics, and therapeutics. The practical component is designed to complement the lecture course and will provide students with experience in a wide range of techniques used in proteomics and genomics.
The lecture component of this unit of study is the same as BCHM3092. Qualified students will attend seminars/practical classes in which more sophisticated topics in proteomics and genomics will be covered.
Textbooks
Kraj A and Silberring J Proteomics Introduction to Methods and Applications Wiley 2008
BINF3101 Bioinformatics Project

Credit points: 6 Teacher/Coordinator: Dr Michael Charleston, Dr Nathan Lo Session: Semester 2 Classes: Meeting with academic supervisor 1hour per week & class meeting 1 hour per week. Prerequisites: 12 credit points from Intermediate Biology, Molecular Biology and Genetics, Biochemistry, Microbiology, Pharmacology Prohibitions: SOFT3700, SOFT3200, INFO3600, BINF3001, COMP3206, SOFT3300, SOFT3600 Assumed knowledge: INFO2110 and (INFO1103 or INFO1903) Assessment: Oral group presentations, individual and group reports (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit will provide students an opportunity to apply the knowledge and practice the skills acquired in the prerequisite and qualifying units, in the context of designing and building a substantial bioinformatics application. Working in groups, students will carry out the full range of activities including requirements capture, analysis and design, coding, testing and documentation.
COMP3520 Operating Systems Internals

Credit points: 6 Session: Semester 1 Classes: Lecture 2 hrs/week; Tutorial 2 hrs/week. Prerequisites: COMP2129 Assessment: Through semester assessment (40%) Final Exam (60%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit will provide a comprehensive dicsussion of relevant OS issues and principles and describe how those principles are put into practice in real operating systems. The contents include internal structure of OS; several ways each major aspect (process scheduling, inter-process communication, memory management, device management, file systems) can be implemented; the performance impact of design choices; case studies of common OS (Linux, MS Windows NT, etc.).
INFO3911 IT Special Project 3A

Credit points: 6 Session: Semester 1 Classes: Meeting 1 hr/week; Project Work - own time 8 hrs/week. Assessment: Through semester assessment (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
Note: Department permission required for enrolment
Note: Enrolment by department permission for students with 85% average in School of IT units plus minimum 75% average in other units
This unit enables talents students with maturing IT knowledge to integrate various IT skills and techniques to carry out projects. These projects are largely research intensive.
INFO3912 IT Special Project 3B

Credit points: 6 Session: Semester 2 Classes: Meeting 1 hr/week; Project Work - own time 8 hrs/week. Assessment: Through semester assessment (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
Note: Department permission required for enrolment
Note: Enrolment by department permission for students with 85% average in School of IT units plus minimum 75% average in other units
This unit enables talents students with maturing IT knowledge to integrate various IT skills and techniques to carry out projects. These projects are



largely research intensive.
STAT3012 Applied Linear Models

Credit points: 6 Session: Semester 1 Classes: Three 1 hour lectures, one 1 hour tutorial and one 1 hour computer laboratories per week. Prerequisites: (STAT2012 or STAT2912) and (MATH1002 or MATH1014 or MATH1902) Prohibitions: STAT3004, STAT3002, STAT3904, STAT3902, STAT3912 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This course will introduce the fundamental concepts of analysis of data from both observational studies and experimental designs using classical linear methods, together with concepts of collection of data and design of experiments. First we will consider linear models and regression methods with diagnostics for checking appropriateness of models. We will look briefly at robust regression methods here. Then we will consider the design and analysis of experiments considering notions of replication, randomization and ideas of factorial designs. Throughout the course we will use the R statistical package to give analyses and graphical displays.
STAT3912 Applied Linear Models (Advanced)

Credit points: 6 Session: Semester 1 Classes: Three 1 hour lectures, one 1 hour tutorial and one 1 hour computer laboratory per week. Prerequisites: (STAT2912 or Credit in STAT2012) and (MATH2061 or MATH2961 or MATH1902) Prohibitions: STAT3904, STAT3004, STAT3002, STAT3012, STAT3902 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit is essentially an Advanced version of STAT3012, with emphasis on the mathematical techniques underlying applied linear models together with proofs of distribution theory based on vector space methods. There will be 3 lectures per week in common with STAT3012 and some advanced material given in a separate advanced tutorial together with more advanced assessment work.
STAT3014 Applied Statistics

Credit points: 6 Session: Semester 2 Classes: Three 1 hour lectures, one 1 hour tutorial and one 1 hour computer laboratory per week. Prerequisites: STAT2012 or STAT2912 Prohibitions: STAT3902, STAT3006, STAT3914, STAT3002 Assumed knowledge: STAT3012 or STAT3912 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit has three distinct but related components: Multivariate analysis; sampling and surveys; and generalised linear models. The first component deals with multivariate data covering simple data reduction techniques like principal components analysis and core multivariate tests including Hotelling's T^2, Mahalanobis' distance and Multivariate Analysis of Variance (MANOVA). The sampling section includes sampling without replacement, stratified sampling, ratio estimation, and cluster sampling. The final section looks at the analysis of categorical data via generalized linear models. Logistic regression and log-linear models will be looked at in some detail along with special techniques for analyzing discrete data with special structure.
STAT3914 Applied Statistics Advanced

Credit points: 6 Session: Semester 2 Classes: Three 1 hour lectures and one 1 hour computer laboratory per week plus an extra hour each week which will alternate between lectures and tutorials. Prerequisites: STAT2912 or credit or better in STAT2012. Prohibitions: STAT3006, STAT3902, STAT3014, STAT3907, STAT3002 Assumed knowledge: STAT3912 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Mode of delivery: Normal (lecture/lab/tutorial) day
This unit is an Advanced version of STAT3014. There will be 3 lectures per week in common with STAT3014. The unit will have extra lectures focusing on multivariate distribution theory developing results for the multivariate normal, partial correlation, the Wishart distribution and Hotelling's T^2. There will also be more advanced tutorial and assessment work associated with this unit.