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CUBE 97 Proceedings
BioMOO: Teaching biology in virtual reality
Clare Sansom,
Department of Crystallography,
Birkbeck College,
Malet St.,
London WC1E 7HX
UK
and Venus Internet Ltd.,
24 Denmark St. London
WC2H 8NJ
UK
e.mail: c.sansom@mail.cryst.bbk.ac.uk
Abstract
Technology first developed for computer-games may sometimes come
to have serious applications. Programs - 'MUDs' (Multi-User Domains)
and object-oriented 'MOOs' - first written for adventure games
have been adapted to create virtual reality environments on the
Internet where students and professionals can meet and collaborate
in real-time. BioMOO, 'the meeting place for biologists on the
Internet' is one of these.
The educational potential of this technology
is now being realised in distance learning courses such as the
Advanced Certificate in 'Principles of Protein Structure using
the Internet' (PPS), based at Birkbeck College, London. In the
PPS course, students and tutors meet in BioMOO to discuss course
material and host seminars where experts discuss their work. The
'BioGate' software has now been developed to provide a multimedia
interface to BioMOO. Demonstration models of some laboratory procedures
are being developed using Java applets.
Introduction: What is a MOO?
Virtual reality software used for text-based multi-player adventure
games, which were first introduced during the early 1980s, is
now being used in education. Users of MUDS, or 'Multi-User Dimensions',
connected to the same computer on the Internet, move around a
common environment and interact directly with each other, and
with objects (for example, by reading and writing notes), in real
time, using, most commonly, a simple text interface. A variant
of this type of program, constructed on object-oriented principles,
is known as a 'MOO' (short for 'MUD, Object-Oriented'). MUDs and
MOOs are a form of synchronous electronic conferencing, as compared
to asynchronous conferencing using, for example, email lists.
People can participate in a MUD or MOO using very simple technology:
to connect to a MOO you only need a text-based terminal or terminal
emulator (vt100 or better), connected to the global Internet,
and the Internet address of the computer running the program.
Usually you will also need to know a specific IP 'port number'
which is allocated to the MOO. Using a program known as a 'client'
will give a more user-friendly text-based interface to a MOO.
Clients exist for Windows (and MS-DOS), Macintosh, Unix workstations,
and some other platforms. A wide range of clients can be freely
downloaded from the Internet. TinyFugue (for Unix), and MudWin
(for Windows) are two of the most widely-used examples. Very recently,
multimedia interfaces have been developed. Some of these simply
integrate the MOO within a Web browser, but others incorporate,
for example, VRML (virtual reality meta-language) to allow three-dimensional
representation of players and objects.
BioMOO: The Biologists' Virtual Meeting Place
'BioMOO', known as 'The Biologists' Virtual Meeting Place' (Anderson, 1994; Sansom, 1997)
is one of a number of MOOs set up to serve a particular professional
community. In the words of one of its founders, Gustavo Glusman,
it is a place for students and professional biologists
"to come meet colleagues in Biology and related fields
and brainstorm, to hold colloquia and conferences, to explore
the serious side of this new medium".
It is physically located in the Weizmann Institute, in Israel;
it was set up in 1993 by Glusman and Jaime Prilusky, the Head
of Bioinformatics there. The novel 'BioGate' multimedia interface
to BioMOO, developed by Glusman, enables users with Java-enabled
web browsers to integrate text-based communication and a Web interface
to BioMOO within a single browser.
There are now about 970 registered BioMOO users. The majority
of these are graduate students, or younger professional biologists,
working in academia, but both senior scientists and those working
in industry form significant minorities. BioMOO users come from
forty-six countries, including, besides all the major Western
countries, many in the former Soviet bloc, Asia and Latin America.
Scientists at the beginning of their careers, like those located
in poorer countries, frequently lack the resources needed to travel
to meetings and form international collaborations. Many scientists
in these positions rely on the Internet to keep in touch with
their peers. Tools such as BioMOO which allow communication to
take place in real time may be particularly important for this
as they can, at best, give a sense of immediacy and of 'being
there'.
The BioMOO virtual-reality environment is modelled on that of
a research centre, the 'BioCenter Building' (Figure 1). This contains
laboratories, offices, seminar rooms, a library and even a coffee
bar. One room, described as 'The GCG HelpDesk', contains information
on the comprehensive bioinformatics software suite, GCG; several
expert users of GCG have set times where they will be available
in that room to answer questions from BioMOO users. The 'Chemistry
Laboratory' contains a Java applet which simulates a titration
experiment. Students of elementary chemistry can use this to learn
about molarity. Other rooms are classrooms for the use of students
and tutors on distance-learning courses. The BioCenter Building
is set in a park containing a zoo. When this is complete, it may
become a very useful repository for zoological information, particularly
about phylogeny.
Figure 1: Map showing some of the main rooms in the 'BioCenter
Building' in BioMOO.
Principles of Protein Structure
For the past three years, Birkbeck College, London, has been running
one of the first accredited graduate-level courses in biochemistry
to be taught entirely over the Internet. This course, 'Principles of Protein Structure' or
'PPS' (Durham, 1995; Sansom, 1996)
leads to an Advanced Certificate from London University, which
is approximately equivalent to half a Master of Science degree.
Students are charged fees, with nineteen students from Poland,
Hungary and Lithuania on the current course being supported by
bursaries from the Open Society Institute. Over 120 students from
twenty-one countries have registered for the two accredited courses.
This course was the winner of a Web Award from the Universities
and Colleges Information Systems Association (UCISA) in 1997.
The syllabus of the PPS course starts with the basic 'building
blocks' of protein structure, the amino acids, and takes the students
through the basic structural motifs found in proteins, amino acid
sequence analysis, and protein biosynthesis, to the structures
and functions of selected important classes of proteins. Skills
with Internet tools and web authoring techniques are also taught.
A unique combination of Internet technologies is used to deliver
the material to students. Diagrams, images, and even animations,
of three-dimensional structures of proteins are provided over
the World Wide Web. The students use molecular visualisation and
modelling software such as Rasmol (Sayle, 1996)
to manipulate the structures for themselves, and self-assessment
quizzes using CGI scripts to test their knowledge. Students, tutors
and voluntary consultants subscribe to email discussion lists
which are used for course administration and informal discussion
related to both the course material and the technology used.
BioMOO is an important feature of the PPS course. Tutorials held
in BioMOO are popular with many of the students. Students and
tutors may simply meet in the 'PPS Base' in BioMOO at pre-arranged
times to discuss course material which can be displayed simultaneously
on the participants' web browsers. Alternatively, an expert may
attend to give a seminar on an aspect of protein structure - for
example, the author of Rasmol, Roger Sayle, may meet a group of
students to answer their questions about its operation. It is
very unlikely that an experienced scientist would be prepared
to travel to hold a 'real-life' tutorial session with a small
group of graduate students. Tutors on the course, based at Birkbeck
College, London, have also used BioMOO to discuss course material
and administrative matters with the network of consultants who
are located throughout the developed world.
One remaining problem with the use of any synchronous conferencing
between continents is that of time-zones. 22 out of 75 students
registered on the 1996 PPS course were based in Australia, New
Zealand, Korea or the USA. Tutorials for this group were often
held in BioMOO at midnight GMT. At this time, the East Coast students
were using their PC at home in the early evening; the West Coast
students were following the tutorial at work on Tuesday afternoon
and students from the Pacific rim were taking part at work on
Wednesday morning. There are not enough students from the Pacific
region on the current course to run such a tutorial group. As
no time can be convenient for every student, BioMOO sessions cannot
be made compulsory and some students may be unavoidably disadvantaged.
BioMOO has also been used in other distance learning courses in
the biological sciences. A one-term course on bioinformatics,
run from the University of Bielefeld in Germany, and a shorter
course on 'Biological Resources on the Internet', run from Singapore,
have both used BioMOO for lectures and discussions. There are
many other educational MUDs and MOOs. Two of these - Diversity
University and the Virtual Online University - take the form of
virtual university campuses which offer resources for a wide range
of courses and conferences. Specialist professional and educational
MOOs include TecfaMOO, for research into educational technology,
and a MOO for students of French where all interaction takes place
in that language.
Future Trends
Until very recently, MOO-type applications have been largely text-based,
simply because real-time multimedia has not been practicable due
to network lag. However, with improvements to computer power and
network bandwidth, this is no longer strictly necessary. Complex
Java applications can be made available within a MOO environment
(for example, to demonstrate laboratory procedures), and VRML
"avatars" can be used to give the environments some
degree of three-dimensionality. Shared whiteboards, which allow
people to modify shared documents in real time (so that, for example,
co-authors in different countries may simultaneously read and
modify the same paper in Word format) should also become more
common over the next few years. The only significant problem is
that, although Internet resources are growing fast, the enormous
rise in worldwide Internet usage means that speed is likely to
remain a limiting factor with Internet-based synchronous communication
and conferencing tools for the foreseeable future.
References
Anderson, C. (1994).
Cyberspace offers chance to do Virtually Real Science. Science
264, 900-901
Durham, A. (1995).
Protein Knowledge at a Click. The Times Higher Education Supplement
(Feb 10 1995) multimedia supplement p. v
Sansom, C. (1996).
Molecular Education on the Web. The Biochemist (Dec/Jan
1995/6), pp. 32-35
Sansom, C. (1997).
BioMOO: The Biologists' Virtual Meeting Place. The Biochemist,
to be published August 1997
Sayle, R. (1996).
RasMol v. 2.6 molecular graphics program. Available via anonymous
ftp from ftp.dcs.ed.ac.uk in directory pub/rasmol
Some Useful URLs
The BioMOO Homepage: http://bioinformatics.weizmann.ac.il/BioMOO/
The BioMOO Page from the Principles of Protein Structure course:
http://pps.cryst.bbk.ac.uk/technology/MOO.html
An Introduction to "MOOing" and BioMOO, by Iddo Freidberg,
Hebrew University of Jerusalem: http://www.ls.huji.ac.il/~idoerg/mooguide.html
List of MOO Clients:
http://tecfa.unige.ch/edu-comp/WWW-VL/eduVR-page.html#Clients
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