BIO 2211 Bioinformatics

STAFFING:

REQUISITES:

OTHER-REQUISITES:

RATIONALE:

Bioinformatics brings together the fields of life science, computer science and statistics. Bioinformaticians are involved in the development of technologies for storing, extracting, organizing, analysing, interpreting and utilizing biological information. With the ever increasing size of genome and other biologial data sets, students are required to extend their knowledge of existing statistical methodologies to the analysis of huge amount of data. Students of bioinformatics gain a better understanding of biological systems by creative application of statistics and computer analysis. Cross-disciplinary knowledge courses are essential to the development of this emerging discipline.

SYNOPSIS:

You will be introduced in an integrated approach to the cross-disciplinary field of Bioinformatics. This course provides an introduction to both theoretical and practical aspects of DNA and protein sequence analysis including the searching of DNA, protein and nucleic acid databases using homology-based and pattern-based search algorithms, as well as sequence comparisons and alignments and evolutionary analysis. You will develop skills in interfacing with and retrieving information from sequence and genome databases and in Perl programming as applied to bioinformatics. Methods of sequence alignment including dynamic programming and the supporting statistical theory are introduced. Topics include collection of sequences, sequence alignment, prediction of RNA secondary structure, phylogenetic relationships, gene prediction and protein structure prediction.

OBJECTIVES:

On completion of this course students will be able to:

1. explain the principles of DNA sequencing and conduct database analyses;
2. predict molecular structures from genetic material;
3. analyse gene homology and predict evolutionary relationships;
4. write and interpret basic Perl programs with application to bioinformatics;
5. apply appropriate statistical tests of significance in relation to the interpretation of output from a range of bioinformatics software;
6. show a high level of skill in the use of informatics techniques with an emphasis on the organisation, display and interrogation of complex data; and
7. describe the limitations of existing techniques.

TOPICS:

TEXT and MATERIALS required to be PURCHASED or accessed:

ALL textbooks and materials are available for purchase from USQ BOOKSHOP (unless otherwise stated). Orders may be placed via secure internet, free fax 1800642453, phone 07 46312742 (within Australia), or mail. Overseas students should fax +61 7 46311743, or phone +61 7 46312742. For costs, further details, and internet ordering, use the 'Textbook Search' facility at http://bookshop.usq.edu.au click 'Semester', then enter your 'Course Code' (no spaces).

REFERENCE MATERIALS:

STUDENT WORKLOAD REQUIREMENTS:

ASSESSMENT DETAILS:

NOTES:

1.

Lecturer will advise due date for Assignment 1

2.

Examiner to advise due date for Assignment 2

3.

Examination dates will be available during the Semester. Please refer to the examination timetable when published.

IMPORTANT ASSESSMENT INFORMATION

1. Attendance requirements:
   There are no attendance requirements for this course. However, it is the students' responsibility to study all material provided to them or required to be accessed by them to maximise their chance of meeting the objectives of the course and to be informed of course-related activities and administration.
2. Requirements for students to complete each assessment item satisfactorily:
   To satisfactorily complete an assessment item a student must achieve at least 50% of the marks or a grade of at least C-. Students do not have to satisfactorily complete each assessment item to be awarded a passing grade in this course. Refer to Statement 4 below for the requirements to receive a passing grade in this course.
3. Penalties for late submission of required work:
   If students submit assignments after the due date without prior approval then a penalty of 20% of the total marks gained by the student for the assignment will apply for each working day late.
4. Requirements for student to be awarded a passing grade in the course:
   To be assured of receiving a passing grade a student must achieve at least 50% of the total weighted marks available for the course. Students who do not qualify for a Passing grade may, at the discretion of the Examiner, be awarded a Supplementary Examination and/or assigned additional work to demonstrate to the Examiner that they have achieved the required standard. It is expected that such students will have gained at least 45% of the total marks available for all summative assessment items. (or be assessed as close to a grade of C- on all summative assessment items.)
5. Method used to combine assessment results to attain final grade:
   The final grades for students will be assigned on the basis of the aggregate of the weighted marks obtained for each of the summative assessment items in the course.
6. Examination information:
   Candidates are allowed access only to specific materials during a Restricted Examination. The only materials that candidates may use in the restricted examination for this course are: writing materials (non-electronic and free from material which could give the student an unfair advantage in the examination); calculators which cannot hold textual information (students must indicate on their examination paper the make and model of any calculator(s) they use during the examination). Students whose first language is not English, may, with the Examiner's approval, take an appropriate non-electronic translation dictionary (but not technical dictionary) into the examination. Students who wish to use a translation dictionary MUST request and receive written approval from the Examiner at least one week before the examination date. Translation dictionaries will be subject to perusal and may be removed from the candidate's possession until appropriate disciplinary action is completed if found to contain material that could give the candidate an unfair advantage.
7. Examination period when Deferred/Supplementary examinations will be held:
   Any Deferred or Supplementary examinations for this course will be held during the next examination period.
8. University Regulations:
   Students should read USQ Regulations 5.1 Definitions, 5.6. Assessment, and 5.10 Academic Misconduct for further information and to avoid actions which might contravene University Regulations. These regulations can be found at the URL http://www.usq.edu.au/corporateservices/calendar/part5.htm or in the current USQ Handbook.

ASSESSMENT NOTES