Purpose of BC327
BC327 is concerned with a variety of bioinformatics tools used by biochemists and molecular biologists in working with DNA and protein sequences. It is designed to provide (a) experience with current research techniques and databases, and (b) an appreciation of underlying theories and strategies.

Assumed background
BC327 builds on concepts of protein structure, molecular genetics and sequence analysis which have been developed in BC207 (Molecular Biochemistry) (or BC212, Biochemistry: Molecular Components of Cells) and BC209 (Molecular Genetics). Internet and computer experience equivalent to that in BC207 is expected.

Teaching mode
The weekly one-hour lecture at 10.00 on Thursdays is used for two primary purposes:
(a) To introduce new techniques and concepts prior to the practical;
(b) To review problems and queries from the previous week's assignment.

The weekly two-hour practicals (computer workshops ) are self paced. Each workshop has an associated written assignment which is due on the day preceding the next lecture. Most new work assumes familiarity with previous work, so it is essential to keep up to date.

• BC327 is a six-credit point subject (#6, 1L2P) and the "average" student can therefore expect to spend an "average" of three hours per week on completion of the assignments outside of the scheduled practical period.
• Many of the internet exercises in BC327 may be done via a Web browser from home, a College, or the Computer Laboratories in the Molecular Biosciences Building.
• Each student will have an individual project from week 2 to week 7, and most of the weekly assignments will represent stages of progress on this project. A tutor will be available in the iLC laboratory during the scheduled practical periods.
• Attendance at all practical sessions is mandatory, and a record of attendance is maintained. If you are unable to attend a scheduled practical, please contact the subject convenor.

Resource material

• Each student must use his or her free University Network Access account on student for email and other UNIX services in BC327. This account must be obtained before the first practical session. See the Client Service desk at the Prentice Centre (a student card is required).
• If you lose your student password, you may obtain another one at the Client Service desk "on the spot" (if possible).
• The Practical Manual for BC327 will be progressively published on the iLC.http://iLC.uq.edu.au/BC327/index.html Keep the Practical Manual open in one Netscape window for reference while working in another window.
• Printed supplements to the Practical Manual will be distributed in lectures.
• Additional resources for BC327 will be published under "RESOURCES" on the BC327 Home page: http://www.biosci.uq.edu.au/Subjects/BC327/BC327resources.html
• BC327 has no required textbook.
• A copy of the 1999 BC327 Semester Exam will be distributed early in the semester.

Computer Laboratories
Practicals will be held in the interactive Learning Centre (iLC) (69-204, 209) using iMacs. The Manager of the iLC is Andrew Noskoff.

Word processing software (Appleworks) is available under the Applications pulldown on the iMacs in the iLC. BC327 students may print relevant documents in the iLC.

In general, you are welcome to use the iLC lab whenever there are spare computers, even if a class is being held. The "iTimetable" of class bookings in the iLC is available via the iLC Home Page: http://iLC.uq.edu.au

In addition to the iLC, the Macintosh computer laboratories (Rooms 143 and 211) in the Molecular Biosciences Building may be used anytime by BC327 students between 9 am and 5 pm, subject to availability and to the permission of the tutor in charge of the room.

Access to the iLC iMac computers AND to the Molecular Biosciences Building Macintosh computers requires the username and password of your Network Access account on the student server at ITS. If your password is missing or lost, you will have to obtain a new password at the Client Service desk of ITS in order to use the computers in the iLC or the Molecular Biosciences Building.

Responsibility
Students are responsible for knowing and following appropriate safety and computer security precautions in the interactive Learning Centre and in the Computer Laboratories in the Molecular Biosciences Building (Rooms 143 and 211). Many of these precautions are spelt out in the Rules of the Teaching Laboratories which are posted in the Computer Laboratories. Food and drink are not allowed in Computer Laboratories.

Departments and Centres are charged approximately $0.20 per Megabyte of incoming internet traffic from outside the University of Queensland. Computers in the Molecular Biosciences Building may be used ONLY for duly assigned projects and must NOT be used for personal Web surfing.

Molecular Biosciences Computer Laboratories
The Molecular Biosciences Computer Laboratories (Rooms 143 and 211) are available to second and third year students enrolled in selected Biochemistry, Microbiology and Parasitology subjects for work on official projects in those subjects. In addition to the scheduled hours, students may work any time between 9 a.m. and 5 p.m. Monday to Friday if computers are available and with the permission of the tutor in charge of the computer lab if a class is present.

Undergraduate students may print on the Laserprinter located in each of the Molecular Biosciences Computer Laboratories. Each student is given 10 free printing credits (pages) per year. Additional printing credits may be purchased from the office of the Department of Biochemistry (Molecular Biosciences Bld) via a special application form accompanied by a receipt from the University.

In case of problems with the Molecular Bioscience computers or printers, fill in a pink FIXIT FORM and put it in the FIXIT Box in the Molecular Biosciences Computer Laboratories.

Assignments
There will be 13 weekly assignments, each of which is due at 5.00 pm on Wednesday (the day preceding the next lecture). Assignments should be placed in the BC327 Box outside Room 158 of the Molecular Biosciences Building. Late or incomplete assignments will not be accepted without sufficient reason, or may attract a penalty.

The marks allotted to assignments total 50% of the semester marks. The marks associated with each assignment vary with the Session:

• Session 1 (no marks).
• Sessions 2-6 (2 marks each), for a total of 10 marks.
• Sessions 7-10 (5 marks each) for a total of 20 marks.
• Sessions 11-13 are used for individual student-selected three-week projects. The assignment for Session 11 is a "2-pager" progress report (2 marks). There is no assignment for Session 12.
• The project report (18 marks) is due on Friday, May 26 (one day after Session 13), at 5.00 pm.

The purpose of the assignments is (a) to encourage regular struggle, and (b) to allow for individual feedback. The early assignments will be marked basically on a pass/fail basis to allow students to develop bioinformatics skills at more or less their own rate. Later assignments involve more integration of concepts and techniques and will therefore be judged more critically.

Assignments will be recorded and handed back at the lecture on the following day whenever possible. Noteworthy points arising from the assignments will be discussed at that lecture. You may be asked to hand in an assignment a second time to correct a major deficiency.

Each assignment must be PROMINENTLY labelled at the top right of the top page with the following information in large letters (biro is OK):

• Name (printed)
• Assignment number (e.g., 2, 7, etc.) Each part of the assignment (e.g., 2A, 7C) should be clearly labelled in BIG letters.

You are welcome to use the clean second side of used paper so long as the irrelevant material is clearly crossed out. In general, please DO NOT use a cover page (Paper is too precious!).

Each assignment should be neatly set out with a title and simple formatting so as to make its message clear. Brief handwritten highlights, explanations and answers to questions are required!

The major part of most assignments will have been copied from a Web page and pasted into a word processing document. Be sure to use a constant width (non-proportional) font such as Courier-10 for all tabular or sequence material which has been taken from a Web. It is good to retain useful, characteristic header information from a Web page because it helps the reader to recognise the source. However, irrelevant material should be removed.

Cooperation and communication with other students in BC327 is strongly encouraged because (a) it helps you to understand the material, and (b) it helps other students to learn. However, the actual assignments must be done individually.

How to contact lecturers in this subject
If you have a question or a suggestion, or if you would like some help, please contact Dr Blakeley by email (blakeley@biosci.uq.edu.au) or in person (Room 158, Molecular Biosciences Building).

Method of Assessment
BC327 is a primarily a practical subject. Assessment will be based on (a) the weekly assignments (50% overall, as detailed above, and (b) on a 1.5-hour Semester Examination (50%).

The Semester Examination will be of the "limited open-book" type, in that each student may bring a double-sided A4 page of his or her own handwritten notes. The examination will involve definitions and bioinformatics problems similar to those in the workshops.

Grade	Criteria
2	Assignments and Semester Examination demonstrate little evidence of effort or understanding.
3	Assignments and Semester Examination demonstrate significant effort and understanding but not at a satisfactory level, given the opportunity that has been offered.
4	Assignments demonstrate a reasonable degree of effort and understanding. Semester Examination demonstrates a moderate capability with definitions, concepts, tools and resources of bioinformatics.
5	As for a mark of 4, except with the additional requirement that the student's semester examination demonstrates substantial understanding of the underlying concepts, tools and resources of bioinformatics which were used in BC32.
6	As for a mark of 5, except with the additional requirement of evidence in the semester examination of some original thought, critical reflection on bioinformatics, or synthesis of reading beyond that directly involved in the practicals.
7	Reserved for excellent work. Criteria incorporate the requirement of a mark of 6 except with the additional requirement of evidence of substantial original thought, critical reflection or synthesis of reading beyond that directly involved in the practicals.