ICT343 (2004) 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. This unit examines computational issues in Molecular Biology and Biotechnology. These range from programming issues and scripting languages, database design, intelligent systems through to the interpretation of data analysis for specific applications. The application areas investigated will include analysis of both animal and plant molecular data with emphasis on comparative studies and genome-wide analysis, functional genomics (microarray data analysis including statistical analysis), proteomics and other post-genomic areas.
Libraries such as BioJava, BioPerl, BioSQL, BioPython and others contain software modules for IO related to biological data (opening, closing, reading, writing, file formats, etc.), analyzing the data, parsing results from analysis, linking data and results to a database, graphical libraries, etc. Then there are significant software development (large projects) that use these various Bio* libraries in an intuitive and constructive way.
This unit provides the students with the ability to learn and discover the open-source world and how it may impact future career opportunities. For this course, we choose life science applications, focusing on the development of bioinformatics solutions using BioPerl.
The unit will focus heavily on the practical application of the BioPerl library. Unit assessment will be primarily based on developing programming solutions to real-world bioinformatics problems. A level of biological knowledge and some experience with the Perl programming language will be an advantage. However, no significant biological knowledge or experience with Perl is required.
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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 and biologists & 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:
- Have a practical understanding of the programming tools used to solve Life Science problems.
- Have an appreciation of advanced Bioinformatics applications.
- Awareness of Open Source Bioinformatic resources.
- An appreciation of the use and application of the Bio-* libraries.
- A basic ability to program in Perl.
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. Lecture can be found on the unit web-site.
Please note that the assignment due dates below are all on Mondays, as oppose to the normal Friday due dates for most units. Extensions to the assignment due dates (only under extremely special unforeseen circumstances) will be announced online.
| Week | Dates | Lecture Topics | Workshop Exercises | Lab Exercises | Assessments Due |
| One | 21 - 25 July | Introduction to ICT343 Introduction to Perl | |||
| Two | 28 July - 01 Aug | More Perl | |||
| Three | 04 - 08 Aug | Introduction to Open Source The Bio-* projects BioPerl | |||
| Four | 11 - 15 Aug | Feature extraction Blast Searches Result Parsing | |||
| Semester Break - 18 - 22 Aug | |||||
| Five | 25 - 29 Aug | Statistics API calls: GC count, sequence size, ... | |||
| Six | 01 - 05 Sep | Sequence Alignment | Assignment 1 Due 1.30pm, Wednesday, Week 6 | ||
| Seven | 08 - 12 Sep | Still more Perl indexes, hashes, pipelines, ... | |||
| Eight | 15 - 19 Sep | SQL BioSQL, DataBase connections, data insertion and retrieval, ... | |||
| Nine | 22 - 26 Sep | Visual/Graphics BioGraphics: generating some nice graphics | |||
| Semester Break - 29 Sep - 10 Oct | |||||
| Ten | 13 - 17 Oct | Pipelines piping results, processing chains, job control, BioMoby, ... | |||
| Eleven | 20 - 24 Oct | Programming and Microarrays | Assignment 2 Due 12pm, Monday, week 11 | ||
| Twelve | 27 - 31 Oct | Open Source Projects, Commercial Bioinformatics and Research. | |||
| Thirteen | 03 - 07 Nov | Exam Revision Wrap up | None | ||
| Study Break - 10 - 14 Nov | |||||
| Examinations Period - 15 - 28 Nov | |||||
Unit Materials
Essential Textbook
None
Highly recommended reading
Tisdall, J., (2001), Beginning Perl for Bioinformatics, O´Reilly & Associates, 1005 Gravenstein Highway, North Sebastopol, Canada 95472. (In closed reserve) Reccomended background 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)
Further reference material may be suggested during each lecture.
Computing Facilities
Internal Students
All lectures, workshops and laboratories will be in ECL 4.034 (linux lab). The laboratory will be available during the normal opening hours of 9am to 5pm. Arrangements to use laboratories outside these hours can be made by seeing the Student 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 three assignments, and the examination.
| Assignment | Description | Value | Due Date</th></tr> | |
| Assignment 1 | TBA | 20% | 12pm, Monday of week 6 | |
| Assignment 2 | TBA | 30% | 12pm, Monday of week 11 | |
| Assignment 3 | Aggregate of set tasks undertaken during the tutorials | 10% | Due by the following weeks tutorial | |
| Examination | Questions on the material from the lectures, workshops and laboratories | 40% | 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 submission For internal students, assignments should be placed in the ICT343 assignment box outside the School of IT corridor in level 3, north wing of ECL building, by 12noon 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 http://www.murdoch.edu.au/admin/legsln/regs/bachelor.html#deferred. 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 a 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 2003 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 DatesStudents 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.
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