ICT238/ICT438 (2006) Overview
Bioinformatics now plays an integral role in the study of fundamental biomedical and agricultural problems. Bioinformatics, which is a new discipline integrating Biology and Information Technology, is now recognised as a core skill for biologists, biotechnologists and IT graduates.
The demand for graduates with Bioinformatics skills is at a critical state world-wide. The job market is growing, and with the supply shortage of graduates with Bioinformatics skills, there are now numerous opportunities for graduates both from IT and Molecular Biology to find work in this new field. The field of Bioinformatics is both challenging and rewarding and is a truly interdisciplinary science.
This course will highlight the computational aspects integral in solving biological problems. Topics covered will include: relevant molecular biology concepts, Bioinformatics terminology, an overview of access to bioinformatics resources via Internet technologies, description of bioinformatics databases and tools to aid in molecular sequence comparison and database searching, gene discovery, identification and characterisation; evolutionary analysis, protein structure analysis, and the design of Bioinformatics strategies to reveal previously unknown relationships with respect to the structure, function, and evolution of genes and proteins.
Contents |
Learning Objectives
Why study Bioinformatics?
Bioinformatics is a new discipline integrating Molecular Biology, Biotechnology and Information Technology. There is an ever increasing job market for bioinformaticians, biologists and IT professionals with bioinformatics skills. Bioinformatics, as a discipline, is now recognised by the Australian Federal Government, in line with the international community, as a strategic area for teaching, research and development.
Bioinformatics, or computational molecular biology, is an interdisciplinary area born from the necessity to deal with exponential growth of all types of biological (molecular) data: to collect, organise, store, and analyse. From an IT perspective, Bioinformatics aims to devise new computational methods and algorithms as well as propose and implement effective information systems to process this information.
Bioinformatics is now integral to understanding the biological, functional and evolutionary significance of the genomic data and the associated computational aspects. This course is aimed at scientists from diverse backgrounds, including: biological, computer, biomedical, agricultural, and physical sciences, engineering, and information systems/technology.
At the end of this unit, you should:
- Understand the fundamental principles of Bioinformatics.
- Possess relevant (rudimentary) knowledge of Genetics and Molecular Biology.
- Possess relevant knowledge of Molecular Evolution.
- Know how to analyse Molecular sequences (using a range of publicly available and proprietary resources).
- Know how to search molecular sequence databases (including understanding of the search algorithms).
- Know how to align molecular sequences (including knowledge of the alignment algorithms).
- Know how to identify genes using Bioinformatics tools.
- Know how to conduct phylogenetic tree analysis (including knowledge of the phylogenetic tree algorithms).
- Know how to analyse protein sequence structure at a basic level.
- Be aware of current scope and limitations of Bioinformatics tools.
- Develop analytical problem solving skills, relevant for Bioinformatics.
Unit Timetable
The following timetable will help you to plan your study over the semester. This schedule for the lecture topics is subject to change during the semester. Lectures can be found on the unit web-site.
Please note that the assignment due dates below are all on Tuesdays, as opposed to the normal Friday due dates for most units. Extensions to the assignment due dates will be only granted under extremely special unforeseen circumstances.
| Week | Lecture Topics | Lab Exercises | Assessments Due |
| One | Introduction to ICT238/ICT438 Introduction to Bioinformatics Comparative Genomics Basic Bioinformatics Internet Resources | Introduction to Internet resources | |
| Two | Introduction to Sequence Comparisons Data storage formats (sequence) Dot Plots Genomic Features | Data storage formats (sequence) Dotplot analysis | |
| Three | Overview of Bioinformatics Resources on the Internet | Getting familiar with Bioinformatics Internet resources | |
| Four | Introduction to database searching, sequence alignment and database searching | Introduction to database searching Sequence Alignment | |
| One-week Semester Break : Assignment 1 (due 12noon Wednesday) | |||
| Five | First practical example of bioinformatics in practice | TBA | |
| Six | Multiple sequence alignment and database searching: statistical interpretation | Multiple Sequence Alignment. | |
| Seven | Introduction to molecular evolution | Phylogenetic Analysis I | |
| One-week Semester Break | |||
| Eight | Introduction to molecular evolution | Phylogenetic Analysis II | |
| Nine | Expression Analysis Genetic microarrays | Introduction to expression analysis | |
| Ten | Introduction to protein sequence and structure analysis | Structure Analysis | |
| Eleven | Large Scale Sequence Alignment The next step | TBA | |
| Twelve | Second practical example of bioinformatics in practice | Using a published example | Assignment 2 (due 12 noon Thursday) |
| Thirteen | Exam Revision Wrap up | None | Assignment 3: Presentation report (due 12 noon Thursday) |
| One-week Study Break | |||
| Examinations Period | |||
The university Calendar for 2006
Unit Materials
Essential Textbook
None
Highly recommended reading
Bioinformatics: Sequence and Genome Analysis by David Mount (Closed reserve)
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins by AD Baxevanis and BF Francis Ouellette (Closed Reserve in Murdoch University Library)
Reference material suggested in each lecture.
Computing Facilities
Internal Students
The laboratory used for this unit will be announced in lectures during the first week of the semester, and is available during normal opening hours of 9am to 5pm. Arrangements to use laboratories outside these hours can be made by seeing the Secretary, ECL Building, room BITL1.02. You will need your Student identity card and a special pass to use the laboratory.
Assessments
Assessment components
You will be assessed on the basis of two assignments, an essay, practical participation in a presentation, and the examination.
| Assignment | Description | Value | Due Date |
| Assignment 1 | TBA | 15% | Wednesday, second break |
| Assignment 2 | TBA | 25% | Tuesday of week 12 |
| Assignment 3 | Presentation and report | 10% | Thursday of week 13 |
| Examination | Questions on materials from lectures, workshops and labs | 50% | Examination period |
Assignments
The questions and descriptions of the assignments may be found on the unit web-site.
Important Note
Please read the section regarding Dishonesty in Assessments and Plagiarism and Collusion below. The unit coordinator and the University views issues of plagiarism very seriously. You may from time to time come across programs and scripts on the web that may be appropriate as solutions for the assignments. Students may not submit such downloaded material for assessment, UNLESS:
1. The student enhances the downloaded material significantly, in line with the unit's objectives (see section 1 of this Unit Outline).
2. The student notifies the unit coordinator BEFORE submitting the work, and fully documents the parts of the work that is theirs.
The reason for allowing students to enhance downloaded work is because most work in Internet development is about building on other people work and components to make better products. What is NOT acceptable is when developers pass work other people work off as their own.
Do not test the unit coordinator's ability to detect plagiarised work when you do not include appropriate acknowledgements. It takes quite considerable effort to modify someone else' work to pass off as your own. All unacknowledged plagiarised work will be passed on the Executive Dean for disciplinary action.
Late submissions
Late assignments will have 10% of the student's final mark for an assignment deducted per day.
Assignment 1
TBA
Assignment 2
TBA
Assignment 3
Presentation and Report
(Internal ICT238 students only, external ICT238 and ICT438 students should consult their documentation or the Unit Coordinator)
During the first week, students will be placed into groups of 3 to 5. Starting in week 8 (after the break)) each group will get a chance to present an aspect of Bioinformatics. Presentation topics are listed below. The first 20 minutes will be used to conduct the presentation. Remaining time may be used for another presentation, further discussion or as a tutorial. Each member of the group will be required to submit (independently) a report on their presentation topic (no more than 1500 words). The marking for this assignment will be broken into two halves with 5% being for the presentation (group work) and the other 5% being for the report (individual).
Based on previous experience with this and other courses, presentations have been a great success. Students found this time beneficial as an open forum to discuss various issues relating to the course. For a "hot" topic such as bioinformatics this is certainly the case. While it may sound daunting to speak in front of the rest of the class, in actual fact it is not, as each student talks for no more than 5 minutes.
The presentation should possess a bioinformatics flavour and include:
- introduction to the relevant area
- outline of general ideas
- current status of the field and/or future directions
- examples
- possible ethical/social implications
- successes/failures in the area
- conclusion with personal views
Presentation Topics
- Human Genome Project
- Genome Sequencing Projects (animal, plant, bacteria)
- Bioinformatics for DNA sequencing (including base calling, editing, etc.)
- Molecular Modelling (homology modelling vs threading)
- Intelligent Systems in Molecular Biology (Artificial Neural Networks and Hidden Markov Models for gene finding, etc)
- New technologies for Bioinformatics (BioPerl, Bio* Projects, distributed objects eg. CORBA)
- New approaches to sequence alignment
- Substitution matrices for sequence alignment
- Bioinformatics and Molecular evolution of viruses, dinosaurs, diseases, comparative studies, specific genes, COGS, etc.
- Statistics for Bioinformatics
- Microarrays
- Single nucleotide polymorphisms and microsattelite markers(SNPs)
- Copyright, ethics, patenting
- Other suggested topics to be approved by the Unit Coordinator
Assignment submission
For internal students, assignments should be placed in the ICT238 assignment box outside the School of IT corridor in level 2, north wing of ECL building, by 12 noon on the due date. The cover sheet with the declaration completed must be attached. Cover sheets for each assignment will be available from the unit web-site.
Assignments are (very occasionally) lost in the Murdoch system, so all students are required to keep copies of their assignments until the end of the appeals period after the semester.
Extensions for assignments will be granted only in exceptional circumstances. If something exceptional arises that requires an extension you should contact the unit coordinator before the deadline expires. Only the unit coordinator can grant extensions.
Important Note
Reasons which are not sufficient to warrant an extension include computer failures; car failures or other transportation difficulties; work conflicts, other study commitments, and dog eating your assignments. "Losing" work through "computer failure" is not accepted as a reason for late submission of an assignment; students using a computer should know to frequently save and backup your work. Also, you should identify conflicts with other work and study commitments at the beginning of semester and schedule your time accordingly. If you are unable to do so, contact the unit coordinator for advice and special arrangements.
Assignment submissions cannot be accepted after the examination has commenced unless deferred assessment on the unit as a whole has been approved. Deferred assessment may be granted in cases of extenuating personal circumstances such as serious personal illness or bereavement. Applications for deferred assessment must be submitted by the end of week 13 of the semester or, in the event of circumstances arising after that date, before the examination. Refer to the current University Handbook for details or online.
Examination
The final examination will be of 3 hours duration and held during the examination period at the end of the semester. It will be closed book exam. The questions in the exam will assess your understanding of the materials in the lectures and labs.
Further guidelines to the examinations, as well as sample examinations will be available on the unit web-site reaching the end of the semester.
The University requires that all students sitting end-of-semester examinations (including those held off-campus) must show their 2006 Murdoch University Student Card to facilitate photographic identification. No other form of identification will be accepted
Students may inspect their marked examination scripts and discuss the marking with the unit coordinator within 14 days of the posting of results (Degree Regulation 43).
Withdrawal Dates
Students who enrol in this unit and subsequently withdraw will have different status appearing on your academic records depending on the withdrawal date. The following are withdrawal dates and their corresponding academic statuses.
- 31st March 2006: HECS census date. Withdrawals after this date incur HECS liability
- Before 31st March 2006: Does not appear on academic record
- From 1st April 2006 to 16th April 2006: Appears as Withdrawn on academic record
- From 17th April 2006: Appears as a Fail on academic record
