The university of bioinformatics

It used to be that biology students would run a mile from anything that smacked of computing. Now, with bio-IT touted as an indispensable element of the life sciences, what's changed?

Several trends are emerging as Australia's tertiary institutes grapple with the challenge of bioinformatics.

As the following snapshot of bioinformatics courses at a variety of Australian universities reveals, the discipline has not yet gained the critical mass to warrant being a degree course in its own right.

At the same time, it spills over existing boundaries between faculties from computer science to biology and biochemistry to medicine and engineering.

That poses a risk of academic turf wars over who should be responsible for bioinformatics, which may slow its progress in the tertiary environment.

Finally, the sector is so hot that competition to find and attract qualified bioinformaticians to teaching posts is going to pose a hurdle for many universities looking to bulk up in bioinformatics.

Here is a quick overview of how some of Australia's leading universities are ramping up their bioinformatics offerings. Melbourne University For five years the Faculty of Medicine has offered a bioinformatics stream for undergraduates majoring in biochemistry. It consists of a dedicated second-year course on macromolecular structure and bioinformatics which complements third-year work on crystallography and NMR methods.

Currently 20 to 25 students are in the stream and some graduates reportedly have gone on to doctoral work in biocomputational fields within the university and at other institutions. The course has no dedicated lectureship and teaching duties are shared between faculty staff including structural biologist Dr Paul Gooley. Queensland University of Technology QUT views bioinformatics as integral to all parts of biological science. It includes bioinformatics concepts starting from the first year of its Bachelor of Biotechnology Innovation and Bachelor of Applied Science degrees.

By the end of year two, students are conversant with accessing and downloading information from global databases and go on to more advanced exercises, especially in year three, says Dr Collet, course coordinator and a senior lecturer.

Three lecturers handled the advanced courses and 10 cover aspects of basic bioinformation skills.

The program has been running about three years and now has about 240 students in second year and 80 to 90 in third year.

Monash University The Biochemistry and Molecular Biology Department at Monash teaches bioinformatics within the parameters of broader science and biology degrees offered through the Faculties of Medicine and Science.

Undergraduates can take an introductory course in bioinformation techniques in the second year of their degree. The third-year subject offers a more in depth approach and includes modules on protein modelling, drug design and the human genome. The stream is tied off by a major six-week annotation project in which students attempt to assign a function to an uncharacterised protein.

The program began three years ago and this year sees 120 students enrolled in the second-year bioinformatics subject and 40 in the third year.

The courses are handled by two lecturers whose activities are focussed primarily on the bioinformatics area. One is bioinformatician Dr James Whisstock, an NHMRC senior research fellow whose group includes several Honours and PhD students researching within the field of bioinformatics. Dr Whisstock is also a member of the Victorian Bioinformatics Consortium.

"It is probably a little too soon to offer an entire degree dedicated to bioinformatics, however our current courses offer an extensive treatment of the subject and Monash is planning to offer additional modules in the near future," Whisstock says.

"Each bioinformatics subject carries a hefty six-point weighting within the Monash degree, and our student feedback indicates we are striking the right balance", he says.

"The course is detailed enough to provide a solid base for those who might later opt to specialise in the field. For those who don't, the work will benefit them in related careers."

University of Western Australia At UWA, bioinformatics shelters under the Faculty of Life and Physical Sciences. It is taught as a stream within the BSc (Informatics) and BSc (Microbiology) degree programs. It is a second-year offering at the moment but will have a third-year component added next year. There are currently 17 students taking the bioinformatics course.

Three lecturers share duties, including the university's director of crystallography, Dr Matthew Wilce, a specialist in structural bioinformatics. The others are drawn from the computer science and pharmacology departments.

The bioinformatics course is divided into three sections, the first is an introduction to databases, the second with algorithms of alignment and database searching and the third with applications to biology in general.

University of Queensland This year sees UQ's first intake of students for an undergraduate program leading to a Bachelor of Science degree in the field of computational biology. It is a three-year course with expectations that most students will proceed along a four-year honours path. Fifty science students have enrolled but will not be required to nominate a specialty area such as bioinformatics in their first year.

The degree course is funded by a Federal government grant awarded two years ago to support six lecturers in computational biology for three-year terms. The university has contributed additional funding to make it into a five-year program and five of the six lectureships have been filled.

Stimulating support for the new degree is a belief by the UQ campus-domiciled Institute for Molecular Bioscience that it will require up to 80 bioinformaticists on its staff within two years.

Filling the lectureships was not a trivial task, says Susan Hamilton, director of studies, Biological and Chemical Sciences. "These type of people are in demand so getting somebody in the strictly bioinformatics area was quite a challenge. We found it difficult to make appointments." Two of the five lecturers were attracted from overseas.

The undergraduate degree is a cross-faculty initiative between the Biological and Chemical Sciences Faculty and the Engineering, Physical Sciences and Architecture Faculty.

University of New South Wales UNSW has a four-year undergraduate engineering degree majoring in bioinformatics. The degree has been running for two years, with a maximum intake of 20 students a year.

Prof Arun Sharma, head of the School of Computer Science and Engineering, said the degree was created from the ground up so that students learn both life sciences and mathematics in the context of each other.

In the first three years students do computing, life sciences and mathematics as well as special courses in bioinformatics, and in the fourth year they do a major research project and based on their performance they can graduate with honours.

Prof Peter Little, of the School of Biotechnology and Biomolecular Sciences, who teaches the life sciences arm of the degree, said the degree was unique because it came out of the engineering faculty.

"Most bioinformatics courses take biologists and train them as computer scientists and we do it the other way around," he said. "It distinguishes us from the other courses.

"Bioinformatics is a necessary part of a biological education and in the future we plan to incorporate bioinformatics modules in existing biology courses. We don't see it as important to have a postgraduate bioinformatics course right now."

University of Sydney The University of Sydney established a BSc in bioinformatics about four years ago. It was conceived in the Department of Computer Science and later moved to the Faculty of Science, where it is now run by a committee that represents the range of computer science and biology departments which contribute to the new course.

Some 16 to 18 students graduated with a BSc in bioinformatics from Sydney last year, including some honours students.

The program is in the process of hiring a professor of bioinformatics, who will be located in the new Medical Foundations Building that is home to SUBIT - Sydney University Biological Information Technology - the major bioinformatics structure on campus.

Proposals are before the university senate for postgraduate bioinformatics courses that will include a certificate in applied science (bioinformatics), a graduate diploma in bioinformatics, and a masters course.

At the moment, responsibility for bioinformatics is split between the faculties of science and medicine.

Other universities Other universities reportedly offering bioinformatics majors in BSc programs are La Trobe University in Victoria and Flinders in South Australia. The Curtin University of Technology in Western Australia has a graduate certificate while ANU, like Melbourne and Monash, reportedly provide bioinformatics as an optional stream in degree programs.

Bioinformatics is described as a minor stream in degrees at Murdoch and the University of Wollongong.

Additional reporting by Daniella Goldberg