UniServe€Science News, Vol. 4, July 1996

Biocomputing at ANGIS: a 24 hour a day Dry Lab


Tim Littlejohn, Head of the Australian Genomic Information Service

In the March 1996 issue of UniServe* Science News, Ian Johnston (Director, UniServe*Science) put out the cry: Bring on `dry' labs! Ian was referring to the use of computer simulations for efficient and cost effective science education. "Dry labs" are a great idea for teaching, and Australia is fortunate in that it has a national 24-hour-a-day, on-line dry lab for molecular biology, genetics and genomics, known as ANGIS.

ANGIS is the "Australian National Genomic Information Service", a national facility that supports the computing needs of biologists. ANGIS provides a core facility with many databases and software packages wrapped under several consistent user-interfaces, accessed through the Internet. There are three interfaces that facilitate access to ANGIS: XANGIS, 2D ANGIS and WebANGIS. XANGIS is a graphical interface, requires X-windows software to be running on your PC or Mac, and can be quite hungry for bandwidth. 2D ANGIS can be accessed through a simple Telnet session, and is much more miserly in its bandwidth, although it offers a text-only interface. WebANGIS is the best of both worlds, offering the graphical, friendly interface of the WWW browser (e.g. Netscape) with the power of ANGIS at a relatively small bandwidth cost.

The primary role of ANGIS is as a research tool; however, a number of universities across the country also use ANGIS as a teaching tool. And this makes a lot of sense. The amount of genetic data being generated around the globe is growing exponentially. Numerous genome programs are adding to this growth, as is the increasing use of molecular-biology methods. Computers offer the only solution to handling this volume of information, resulting in the birth of a new discipline, "bioinformatics", the application of computers to solving problems in biology (the Australian bioinformatics community meets through ABnet, the Australian Bioinformatics Network; see http://www.angis.su.oz.au/ ABnet/about.html).

From a biology teachers perspective, however, the real beauty of the ANGIS dry lab is that it is not a simulation . The software, databases and interfaces the students use are the very same ones used by the scientists in Universities, hospitals, CSIRO and industry. Thus, while bioinformatics classes have all the benefits of "dry-labs" in the sense used by Ian Johnston, they have the additional benefits of allowing the students to use the tools, and do the computer-based experiments, exactly as they will do when they graduate.

ANGIS is used to teach many concepts in biology: evolution, gene structure, genome organisation, genetic linkage and protein structure, for example. These concepts cross many discipline boundaries: medicine, genetics, zoology, biochemistry, botany, physiology, pharmacology, and many others. Dedicated genome databases allow academics to choose their preferred organism: the complete genomes of two bacteria and of the brewers yeast are available, and graphical genome databases for flies, worms, plants and humans are all accessible through ANGIS. The software tools residing on ANGIS are generally used to analyse molecular data (DNA and protein sequences, for example). However, many of these tools are not restricted to molecular or genomic data. For example, the genetic linkage software on ANGIS can be used on any sets of markers, and a phylogenetic analysis package on ANGIS ("PHYLIP") can cope with continuous traits derived from any method.

ANGIS supports its subscribers through telephone and email, offers training courses on use of the system, and provides documentation and printed tutorials. ANGIS is working with groups around the country that use the facility as a teaching tool so that it can closely meet the needs of educators. ANGIS also acts as a conduit between these groups, so that educators can communicate, share teaching material, and minimise duplication of effort.

As access to the Internet becomes even more widespread, and WWW browsers become the preferred tool for interacting with the Internet, resources such as WebANGIS will become a powerful tool for educators. Learning time can be spent on the biology, not on the software, as familiarity with the standard browser interface is assured. As the Internet creeps down the phone lines into student's homes, expect to see more and more students discovering and exploring their interests in biology in their own space and time through resources such as WebANGIS. In this way WebANGIS could be used for distance education, tele-classes, out of class assignments and other innovative teaching approaches.

Tim Littlejohn

Australian Genomic Information Service
Building J03
University of Sydney,
Sydney, NSW, 2006
email: tim@angis.su.oz.au
Phone/Fax: 61-2-9 351 2948

Cost: For an academic department costs start at $1150/year. This includes access to all tolls, unlimited support, documentation, and access to courses and workshops.

Screen shot from the ANGIS web site.