Paper submitted to the World Conference on Educational Media,
Hypermedia and Telecommunications (ED-MEDIA 99), June 19-24, 1999, Seattle,
The Virtual Cell: An Interactive, Virtual Environment for Cell Biology
Alan R White1
Phillip E. McClean2
and Brian M. Slator3
and Computer Science3
North Dakota State University, Fargo, ND 58105
The Virtual Cell is an interactive, 3-dimensional visualization of a bio-environment. It has been
prototyped using the Virtual Reality Modeling Language (VRML), and is to be available via the Internet.
To the student, the Virtual Cell looks like an enormous navigable space populated with 3D organelles. In
this environment, experimental goals in the form of question-based assignments promote deductive
reasoning and problem-solving in an authentic visualized context. The NDSU WorldWide Web
Instructional Committee (WWWIC) is engaged in developing a range of irtual environments for
education. These projects span a range of disciplines, from Earth Science to Anthropology, and from
Business to Biology. However, all of these projects share a strategy, a set of assumptions, an approach
to assessment, and an emerging tool set, which allows each to leverage from the insights and advances
of the others.
The Virtual Cell is being developed by the NDSU World Wide Web Instructional Committee
(WWWIC), a multi-disciplinary group of faculty engaged in the development of virtual/visual worlds for
science education (NDSU's WWWIC). Other WWWIC projects include The Geology Explorer, The Visual
Computer Program and ProgrammingLand MOO. Each of these projects share a common objective: to teach scientific
problem-solving skills (deductive reasoning, experimental design, hypothesis formation) through
immersion in learn-by-doing virtual environments. These projects are designed to support
discovery-based learning in a self-paced, role-based, and goal-oriented framework. They are also
learner oriented, immersive, and exploratory in nature. Each project aims toward highly interactive,
highly graphical systems employing software tutors to guide and remediate in the event of student
failure. In addition, each project individually pursues the objective of teaching discipline-specific science
content through the achievement of authentic problem-solving goals, but using uniquely different
approaches. The projects are designed to employ consistent elements across disciplines and, as a
consequence, foster the sharing of development plans and development tools. More information about
WWWIC is available at http://www.ndsu.nodak.edu/wwwic/.
Learning by Doing
The goal of post-secondary science education is to
train future scientists. One problem with science education is the standard lecture/laboratory format. In
lecture the professor speaks, and the student passively listens. In the worst case, lectures are no better
for learning than television: a totally passive, non-interactive experience. Meanwhile, laboratories are
intended to afford students with an interactive, experimental experience, but in reality these are usually
rigidly structured by the laboratory outline where the intended outcome is known and the procedure is
inflexible. These are not experimental experiences. If laboratories were to be truly experimental,
question- and hypothesis-driven experiences, then students would need access to modern laboratory
equipment and instrumentation, a vast array of expensive laboratory reagents, and a wealth of instructor
time that the university cannot possibly afford. Active learning can be expensive, yet the value of active
versus passive learning has become increasingly clear (Reid, 1994).
Science students need an interactive, exploration-based learning experience that teaches
basic principles. Hypertext, CD-ROM presentations, and world wide web pages can make a contribution
to active learning. The learner has control over many aspects of the presentation by deciding which
pages to visit and in what order. However, these are non-experimental approaches that mimic a book.
Browsing through hypertext is still a two-dimensional, non-interactive, and largely passive activity. An
active learning alternative is the virtual environment or world where learners can experience their
education in a "learning-by-doing" way. Student visitors are invited to participate in a self-paced
exploration of the environment, where they can make observations, manipulate the interactive objects,
and design and perform experiments. We are developing such a virtual world, The Virtual Cell, that
enables exploratory, hypothesis-driven, and experimental science learning.
The Virtual Cell
The Virtual Cell is a virtual, multi-user space where students
"fly" around and practice being cell biologists in a role-based, goal-oriented environment. Working
individually, or with others, students learn fundamental concepts of cell biology and strategies for
deductive problem solving through their experiences in the exploratory environment. This pedagogical
approach gives students an authentic experience that includes elements of practical, experimental
design and decision making, while introducing them to discipline content. By practical applications of the
scientific method, students learn how to think, act, and react as cell biologists (Slator and Chaput, 1996).
The Virtual Cell is a 3D environment in which the student can learn about the structure and
function of a cell. The Virtual Cell is populated with subcellular components: nucleus, endoplasmic
reticulum, Golgi apparatus, mitochondria, chloroplast and vacuoles. Each structure is rendered as a 3D
object using the Virtual Reality Modeling Language (VRML), a computer language for specifying three-
dimensional worlds that can be displayed and, most importantly, interacted with via the Internet. The
Virtual Cell development project can be visited at
The Virtual Cell Experience: The Laboratory
The Virtual Cell consists of a VRML-based laboratory and a cell. In the laboratory, the learner
receives a specific assignment (learners are always assigned motivating goals in our learning-by-doing
environments), performs simple experiments, and learns the basic physical and chemical features of the
cell and its components. The virtual laboratory procedures require a voyage into a VRML cell (see
below), where experimental science meets virtual reality. The learner is supplied with a toolbox of
measuring devices that assay various cellular processes. These tools include an O2 meter,
CO2 meter, pH meter, sugar assay, protein assay, various stains and enzyme assays. As
the students progress, they revisit the laboratory, bring cellular samples back for experimentation, and
subsequently receive more assignments.
Student understanding of the concepts related to the structure and function of the cell is an
essential feature of the pedagogy of modern biology. Learning the physical components of the cell, how
these components interact, and how these interactions are regulated has largely replaced the traditional
organismal approach to teaching biology. The cell, though, is a complex, multidimensional environment
where time and space are critical factors that determine when and where cellular events occur. It is very
difficult to capture this multi-dimensionality in the 2-D space of the printed page, chalk board, or web
The virtual cell contains 3D representations of all the
components and organelles of a cell (nucleus, mitochondria, chloroplasts, etc). The user "flies" among
these organelles and uses virtual instruments to conduct experiments. All navigation is learner directed;
there is no predetermined exploratory path. This feature empowers the student to direct their own
learning. The student is also able to travel into linked VRML worlds that represent the interior of each of
the cellular organelles. Further experimentation inside each organelle allows the student to learn about
their specific functions (Wu, 1998).
For example, the learner may confront the nucleus and perform several simple experiments.
The nucleus is not consuming or generating O2 or CO2, it has a positive
Fulgen stain reaction and it demonstrates a negative luciferase enzyme reaction. The learner must put
these results into a context. They would have to learn from a lecture, a textbook or a tutoring agent that
a positive Fulgen stain means DNA is present and a negative luciferase reaction means ATP is absent.
In the cell, this general information is contained in the 3D representation and offered via touch sensitive
points. Putting this and information from additional experiments together, the learner should deduce that
the object is the nucleus and that DNA is contained there. Additional pertinent data about the nucleus
and other cellular organelles can be collected in the same manner.
More advanced levels of the Virtual Cell include the
introduction of cellular perturbations and the investigation of the functions of various cellular structures or
processes. In the second level, a simulation will change the cell by either introducing a mutation or
adding an inhibitor that disrupts a cellular process. An alarm will sound, some cellular process will
malfunction, and the learner will be given the goal of diagnosing the problem. Using the same tools as in
the previous level, the learner will navigate through the cell, make observations, and perform
measurements and experiments. The learner will attempt to identify the affected area, the perturbed
process, and the nature of the mutation or inhibitor that is causing the problem. As a result, the user will
learn details of cellular processes and functions and become familiar with the importance of various
mutations and inhibitors for cell biology experimentation.
In the third level of the Virtual Cell, the learner will be given a set of goals to investigate a
specific cellular structure or process. The learner will have at their disposal the tools from the first level
and the mutations and inhibitors from the second level. Using these in various combinations, the student
will form hypotheses, design experiments, and employ the toolbox items to perform these experiments.
For example, the learner might be given the goal of determining how a membrane vesicle buds off from
one compartment and is specifically targeted to fuse with another compartment. Using the tools from
previous levels and their experience with designing and performing experiments, the learner could
determine that proteins from two compartments recognize each other, bind in a specific fashion, and
promote the fusion of a vesicle to a target compartment.
The implementation of the Virtual Cell depends on coordinating three technologies: 1) VRML
visualization, 2) a text-based MOO server (Curtis, 1992), and 3) Java client and simulation software.
Students will use a standard WWW browser to launch a Java applet, which will provide a connection to
an object-oriented, multi-user domain (a MOO; see below) where cellular processes are simulated and
multi-user viewpoints are synchronized. The Java applet also launches an interface to the VRML
representation of the Virtual Cell, allowing the student to explore and experiment within the 3D
representation. To the student, the Virtual Cell will look like an enormous navigable space where
deductive reasoning and problem-solving in a visualized context are necessary for completion of
assigned experimental goals.
The object-oriented multi-user domain (MOO) simulation on which the cell is established
allows students to interact directly with one another within the cell, providing advice to one another or
even working together to achieve particular goals. Because the MOO is internet-based, students from
separate and distant locations can simultaneously interact with the cell and with one another. Unintrusive
but proactive software agents act as tutors, monitoring students' actions and "visiting" the students as the
need arises. Tutor agents provide advice on equipment choices, navigation, and scientific conclusions.
Tutors neither mandate or insist on student actions nor do they block or prevent student actions.
The Virtual Cell is an attempt by science educators to develop educational tools and methods
that deliver the principles but also teach important content information in a meaningful way to biology
students. Virtual classrooms and virtual laboratories help solve many of the problems faced in
secondary and post-secondary education: distance learning becomes a reality, learner diversity is
accommodated (both in terms of learning styles and life styles), and in many cases the curriculum
becomes more active, more role-based, more self-paced, and more "learn by doing" than "learn by
- Curtis, Pavel (1992). Mudding: Social Phenomena in Text-Based Virtual Realities. Proceedings of
the conference on Directions and Implications of Advanced Computing (sponsored by Computer
Professionals for Social Responsibility)
- Reid , T Alex (1994) Perspectives on computers in education: the promise, the pain, the prospect.
Active Learning. 1(1), Dec. CTI Support Service. Oxford, UK
- Slator, Brian M. and Harold "Cliff" Chaput (1996) Learning by Learning Roles: a virtual role-playing
environment for tutoring. Proceedings of the Third International Conference on Intelligent Tutoring
Systems (ITS'96). Montreal: Springer-Verlag, June 12-14, pp. 668-676. (Lecture Notes in Computer
Science, edited by C. Frasson, G. Gauthier, A. Lesgold)
- Wu, Yihe (1998) Simulation of the Biological Process of Steroid Hormones with VRML. M.S.
Thesis. North Dakota State University, Fargo, ND
Development of the Virtual Cell is funded by the National Science Foundation under
grants DUE-9752548. For further information on virtual worlds software development at North Dakota
State University, visit the NDSU WWWIC web site.
The authors acknowledge the large team of dedicated undergraduate and graduate students in the
computer and biological sciences who have made this project so successful. © 1998 World
Wide Web Instructional Committee.