University of Sydney Handbooks - 2013 Archive

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Table 1: Bioinformatics

Table 1 lists units of study available to students in the Bachelor of Science and combined degrees. The units are available to students enrolled in other degrees in accordance with their degree resolutions.

Unit of study Credit points A: Assumed knowledge P: Prerequisites C: Corequisites N: Prohibition Session

Bioinformatics

For a major in Bioinformatics, students must complete a minimum of 24 credit points from senior units of study in the Life Sciences, Statistics, and Information Technologies, including:-
(i) At least one of BIOL3018/3918, BIOL3025/3925, BIOL3026/3926, BCHM3092/3992; and
(ii) At least one of STAT3012/3912 and STAT3014/3914; and
(iii) COMP3456; and
(iv) BINF3101
For further information on how to prepare for a major in Bioinformatics, please consult the Faculty of Science's web page (http://www.science.usyd.edu.au/fstudent/undergrad/course/)
Bioinformatics major (A) units of study
BIOL3018
Gene Technology and Genomics
6    P 12 credit points from MBLG2071, MBLG2971, MBLG2072, MBLG2972 and Intermediate Biology units. For BMedSc students: either (a) 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units OR (b) 12 credit points of Intermediate BMED units, including BMED2802
N BIOL3918
Semester 1
BIOL3918
Gene Technology and Genomics Advanced
6    P Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units. For BMedSc students: either (a) Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units OR (b) Distinction average in 12 credit points of Intermediate BMED units, including BMED2802.
N BIOL3018
Semester 1
BIOL3025
Evolutionary Genetics & Animal Behaviour
6    P 12 credit points from (MBLG2071/MBLG2971), (MBLG2072/MBLG2972) or Intermediate Biology or Intermediate PLNT units. For BMedSc students: 30 credit points of Intermediate BMED units including BMED2802 or BMED2401.
N BIOL3925
Semester 2
BIOL3925
Evolutionary Gen. & Animal Behaviour Adv
6    P Distinction average in12 credit points from (MBLG2071/MBLG2971), (MBLG2072/MBLG2972) or Intermediate Biology or PLNTunits. For BMedSc students: 30 credit points of Intermediate BMED units including Distinction in either BMED2802 or BMED2401.
N BIOL3025
Semester 2
BIOL3026
Developmental Genetics
6    P 12 credit points from MBLG2071, MBLG2971, MBLG2072. For BMedSc students: either (a) 12 credit points from MBLG2071/2971, MBLG2072/2972 OR (b) 12 credit points of Intermediate BMED units, including BMED2802.
N BIOL3926
Semester 2
BIOL3926
Developmental Genetics (Advanced)
6    P Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972. For BMedSc students: either (a) Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 OR (b) Distinction average in 12 credit points of Intermediate BMED units, including BMED2802.
N BIOL3026
Semester 2
BCHM3092
Proteomics and Functional Genomics
6    P (MBLG1001 or MBLG1901) and 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/MBLG2971 or BCHM2071/BCHM2971 or BCHM2072/BCHM2972). For BMedSci: (18 credit points of BMED including BMED2401 and BMED2405 and one of MBLG2701 or MBLG2971 or BCHM2071 or BCHM2971) OR (BMED2801 and BMED2802 and BMED2804).
N BCHM3992
Semester 2
BCHM3992
Proteomics and Functional Genomics (Adv)
6    P (MBLG1001 or MBLG1901) and Distinction in 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/MBLG2971 or BCHM2071/BCHM2971 or BCHM2072/BCHM2972). For BMedSci: (18 credit points of BMED including BMED2401 and Distinction in BMED2405 and one of MBLG2701 or MBLG2971 or BCHM2071 or BCHM2971) OR (Distinction average in BMED2801 and BMED2802 and BMED2804).
N BCHM3092
Semester 2
Bioinformatics major (B) units of study
STAT3012
Applied Linear Models
6    P (STAT2012 or STAT2912 or STAT2004) and (MATH1002 or MATH1014 or MATH1902)
N STAT3912, STAT3002, STAT3902, STAT3004, STAT3904
Semester 1
STAT3912
Applied Linear Models (Advanced)
6    P (STAT2912 or Credit in STAT2004 or Credit in STAT2012) and (MATH2061 or MATH2961 or MATH1902)
N STAT3012, STAT3002, STAT3902, STAT3004, STAT3904
Semester 1
STAT3014
Applied Statistics
6    A STAT3012 or STAT3912
P STAT2012 or STAT2912 or STAT2004
N STAT3914, STAT3002, STAT3902, STAT3006
Semester 2
STAT3914
Applied Statistics Advanced
6    A STAT3912
P STAT2912 or credit or better in (STAT2004 or STAT2012).
N STAT3014, STAT3002, STAT3902, STAT3006, STAT3907
Semester 2
Bioinformatics major (C) unit of study
COMP3456
Computational Methods for Life Sciences
6    P (INFO1105 or INFO1905) and (COMP2007 or INFO2120) and 6 credit points from BIOL or MBLG
Semester 2
Bioinformatics major (D) unit of study
BINF3101
Bioinformatics Project
6    A INFO2110 and (INFO1103 or INFO1903)
P 12 credit points from Intermediate Biology, Molecular Biology and Genetics, Biochemistry, Microbiology, Pharmacology
N COMP3206, BINF3001, INFO3600, SOFT3300, SOFT3600, SOFT3200, SOFT3700
Semester 2

Bioinformatics

For a major in Bioinformatics, students must complete a minimum of 24 credit points from senior units of study in the Life Sciences, Statistics, and Information Technologies, including:-
(i) At least one of BIOL3018/3918, BIOL3025/3925, BIOL3026/3926, BCHM3092/3992; and
(ii) At least one of STAT3012/3912 and STAT3014/3914; and
(iii) COMP3456; and
(iv) BINF3101
For further information on how to prepare for a major in Bioinformatics, please consult the Faculty of Science's web page (http://www.science.usyd.edu.au/fstudent/undergrad/course/)
Bioinformatics major (A) units of study
BIOL3018 Gene Technology and Genomics

Credit points: 6 Teacher/Coordinator: A/Prof Neville Firth Session: Semester 1 Classes: 2x1 hr lectures/week, 1x3 hr practical/week. Prerequisites: 12 credit points from MBLG2071, MBLG2971, MBLG2072, MBLG2972 and Intermediate Biology units. For BMedSc students: either (a) 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units OR (b) 12 credit points of Intermediate BMED units, including BMED2802 Prohibitions: BIOL3918 Assessment: 2 hr exam (60%), assignments (40%) Associated degrees: B An Vet Bio Sc, B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), B Sc (Molecular Biotechnology), UG Study Abroad Program.
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 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, the transformation of animal and plant cells, the genetic engineering of animals and plants, and the environmental release of genetically-modified (transgenic) organisms. 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: 2x1 hr lectures/week, 1x3 hr practical/week. Prerequisites: Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units. For BMedSc students: either (a) Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 and Intermediate Biology units OR (b) Distinction average in 12 credit points of Intermediate BMED units, including BMED2802. Prohibitions: BIOL3018 Assessment: 2 hr exam (60%), assignments (40%) Associated degrees: B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), B Sc (Molecular Biotechnology), UG Study Abroad Program.
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.
BIOL3025 Evolutionary Genetics & Animal Behaviour

Credit points: 6 Teacher/Coordinator: Prof Oldroyd, A/Prof Beekman. Session: Semester 2 Classes: 2x1 hr lectures/week, 1x4 hr practical/week. Prerequisites: 12 credit points from (MBLG2071/MBLG2971), (MBLG2072/MBLG2972) or Intermediate Biology or Intermediate PLNT units. For BMedSc students: 30 credit points of Intermediate BMED units including BMED2802 or BMED2401. Prohibitions: BIOL3925 Assessment: 1x1.5 hour exam, assignments, seminar (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), UG Study Abroad Program.
The unit of study covers the main themes of modern evolutionary theory including population genetics. In the practicals, students use molecular methods to quantify genetic variation in natural populations. Using these skills we will search for population subdivision and discuss how this can lead to speciation. Lectures will cover how the evolution of traits can be tracked using the comparative method. We will consider how studies of sex ratios, sexual selection, kin selection, game theory and quantitative genetics can illuminate the mechanisms by which animals have evolved, and explain why they behave as they do. We will then consider if these themes have any relevance to human sociobiology. The unit also covers the role of genetics in conservation. There will be a field trip to collect organisms for population genetic analysis. There will be plenty of opportunity in the student seminars to examine the more controversial aspects of modern evolutionary thought.
BIOL3925 Evolutionary Gen. & Animal Behaviour Adv

Credit points: 6 Teacher/Coordinator: Prof B Oldroyd, A/Prof Beekman. Session: Semester 2 Classes: 2x1 hr lectures/week, 1x4 hr practical/week. Prerequisites: Distinction average in12 credit points from (MBLG2071/MBLG2971), (MBLG2072/MBLG2972) or Intermediate Biology or PLNTunits. For BMedSc students: 30 credit points of Intermediate BMED units including Distinction in either BMED2802 or BMED2401. Prohibitions: BIOL3025 Assessment: 1x1.5 hr exam, assignments, seminar (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), UG Study Abroad Program.
Qualified students will participate in alternative components of BIOL3025 Evolutionary Genetics and Animal Behaviour. The content and nature of these components may vary from year to year. Some assessment will be in an alternative format to components of BIOL3025.
BIOL3026 Developmental Genetics

Credit points: 6 Teacher/Coordinator: Dr Mary Byrne, Dr J Saleeba Session: Semester 2 Classes: Twenty-four 1 hour lectures/tutorials per semester and up to 3 hours laboratory per week Prerequisites: 12 credit points from MBLG2071, MBLG2971, MBLG2072. For BMedSc students: either (a) 12 credit points from MBLG2071/2971, MBLG2072/2972 OR (b) 12 credit points of Intermediate BMED units, including BMED2802. Prohibitions: BIOL3926 Assessment: 1x2 hr exam, assignments (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), UG Study Abroad Program.
This unit discusses major concepts and current understanding of developmental biology with an emphasis on molecular genetics. The developmental genetics of model plant and animal systems, and approaches used to determine how a complex multicellular organism is established from a single cell, will be investigated. Topics to be discussed will cover a broad range of developmental genetics in animal species, using examples from the model species Drosophila, C. elegans, and mouse. Plant specific processes such as leaf, root and flower development will also be covered. using examples from the model species Arabidopsis. The study of mutants in development will be used to highlight pattern formation, gene interactions and the importance of regulated gene expression in development. Reference will be made to the use of modern techniques in developmental biology such as transgenics, recombinant DNA technology, and 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: Dr M Byrne Session: Semester 2 Classes: Twenty-four 1 hour lectures/tutorials per semester and up to 3 hours laboratory per week. Prerequisites: Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972. For BMedSc students: either (a) Distinction average in 12 credit points from MBLG2071/2971, MBLG2072/2972 OR (b) Distinction average in 12 credit points of Intermediate BMED units, including BMED2802. Prohibitions: BIOL3026 Assessment: 1x2 hr exam, assignments (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Marine Science), B Sc (Molecular Biology & Genetics), UG Study Abroad Program.
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.
BCHM3092 Proteomics and Functional Genomics

Credit points: 6 Teacher/Coordinator: A/Prof Stuart Cordwell, Mrs Jill Johnston Session: Semester 2 Classes: Two 1-hour lectures per week and one 3-hour practical per week. Prerequisites: (MBLG1001 or MBLG1901) and 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/MBLG2971 or BCHM2071/BCHM2971 or BCHM2072/BCHM2972). For BMedSci: (18 credit points of BMED including BMED2401 and BMED2405 and one of MBLG2701 or MBLG2971 or BCHM2071 or BCHM2971) OR (BMED2801 and BMED2802 and BMED2804). Prohibitions: BCHM3992 Assessment: One 2.5-hour exam, practical work (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Molecular Biology & Genetics), B Sc (Molecular Biotechnology), UG Study Abroad Program.
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, Mrs Jill Johnston Session: Semester 2 Classes: Two 1-hour lectures per week and one 3-hour practical per fortnight. Prerequisites: (MBLG1001 or MBLG1901) and Distinction in 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/MBLG2971 or BCHM2071/BCHM2971 or BCHM2072/BCHM2972). For BMedSci: (18 credit points of BMED including BMED2401 and Distinction in BMED2405 and one of MBLG2701 or MBLG2971 or BCHM2071 or BCHM2971) OR (Distinction average in BMED2801 and BMED2802 and BMED2804). Prohibitions: BCHM3092 Assessment: One 2.5-hour exam, practical work (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, B Sc (Molecular Biology & Genetics), B Sc (Molecular Biotechnology), UG Study Abroad Program.
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
Bioinformatics major (B) units of study
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 or STAT2004) and (MATH1002 or MATH1014 or MATH1902) Prohibitions: STAT3912, STAT3002, STAT3902, STAT3004, STAT3904 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Res Ec, B Sc, UG Study Abroad Program.
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 STAT2004 or Credit in STAT2012) and (MATH2061 or MATH2961 or MATH1902) Prohibitions: STAT3012, STAT3002, STAT3902, STAT3004, STAT3904 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, UG Study Abroad Program.
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 or STAT2004 Prohibitions: STAT3914, STAT3002, STAT3902, STAT3006 Assumed knowledge: STAT3012 or STAT3912 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Res Ec, B Sc, UG Study Abroad Program.
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 (STAT2004 or STAT2012). Prohibitions: STAT3014, STAT3002, STAT3902, STAT3006, STAT3907 Assumed knowledge: STAT3912 Assessment: One 2 hour exam, assignments and/or quizzes, and computer practical reports (100%) Associated degrees: B A, B A (Adv)(Hons), B A (Adv)(Hons), M B B S, B Med Sc, B Sc, UG Study Abroad Program.
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.
Bioinformatics major (C) unit of study
COMP3456 Computational Methods for Life Sciences

Credit points: 6 Session: Semester 2 Classes: (Lec 2hrs & Prac 2hrs) per week Prerequisites: (INFO1105 or INFO1905) and (COMP2007 or INFO2120) and 6 credit points from BIOL or MBLG Assessment: Assignment (20%), quizzes(10%) and final exam (70%). Associated degrees: B E, B Med Sc, B Sc.
This unit introduces the algorithmic principles driving advances in the life sciences. It discusses biological and algorithmic ideas together, linking issues in computer science and biology and thus is suitable for students in both disciplines. Students will learn algorithm design and analysis techniques to solve practical problems in biology.
Bioinformatics major (D) unit of study
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: COMP3206, BINF3001, INFO3600, SOFT3300, SOFT3600, SOFT3200, SOFT3700 Assumed knowledge: INFO2110 and (INFO1103 or INFO1903) Assessment: Oral group presentations, individual and group reports (100%) Associated degrees: B Med Sc, B Sc.
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.