Biology Education Software FAQ (1 of 3)

Eli Meir meir at
Fri Oct 27 20:30:54 EST 1995

Biology Education Software FAQ
©Copyright 1995 by Eli Meir and the Biology Education Software
Taskforce of the 
					University of Washington
All Rights Reserved

This document is freely redistributable as long as absolutely no money
is charged and no 
changes are made to the document.

(1)  What is in this FAQ?
	(1a)	Who is B.E.S.T. ?
	(1b)	Where to address comments, queries, etc..
	(1c)	How we picked software to include here
	(1d) 	What information we include about each piece of software we
	(1e)	How to submit software for inclusion on this list

(2)  Resources for information on biology education software
	(2a)	BioQuest
	(2b)	CTI Centre for Biology
	(2c)	NECUSE Biology Software Reviews
	(2d)	Quarterly Review of Biology

(3)  Ecology and Evolution Software
	(3a)	Biota
	(3b)	Environmental Decision Making
	(3c)	Evolve
	(3d)	PopGen / Simul8
	(3e)	Blind Watchmaker
	(3f)	Environmental Science Stella Stacks
	(3g)	Simlife
	(3h)	Populus
	(3i)	PopDyn
	(3j)	Fish Farm

(4)  Physiology and Neurobiology
	(4a)	Neuro 140
	(4b)	Axon
	(4c)	Isolated Heart Laboratories
	(4d)	Neurosim II
	(4e)	Frog Dissection and other dissection tutorials
	(4f)	Interactive Frog Dissection
	(4g)	NeuroLab
	(4h)	SymBioSys
	(4i)	Quantitative Circulatory Physiology
	(4j)	Brainiac

(5)  Cell, Molecular Biology and Genetics
	(5a)	Genetics Construction Kit
	(5b)	Virtual Fly Lab
	(5c)	SequenceIt!
	(5d)	PurifyIt!
	(5e)	RateIt!
	(5f)	Enzyme
	(5g)	MacMolecule
	(5h)	Visual Genetics
	(5i)	Virtual Genetics Laboratory
	(5j)	Photosynthesis Multimedia Textbook
	(5k)	Enzyme Kinetics Stella Stack

(6)  General purpose software useful in education
	(6a)	Stella
	(6b)	Extend
	(6c)	Mathematica
	(6d)	Maple
	(6e)	Matlab
	(6f)	LabView
	(6g)	SuperScope
	(6h)	Spike Studio

(7)  Textbooks on CD

(8)  Mosaic sites and other random stuff
	(8a)	Institute for Molecular Virology 
	(8b)	BioCatalog
	(8c)	Neurosciences on the Internet
	(8d)	Quantitative Training for Life Sciences

(9)  Acknowledments


(1a)  Who is B.E.S.T.

B.E.S.T.  stands for Biology Education Software Taskforce of the
University of Washington.  We are not quite as official as that title
makes us sound, but have done quite a bit of work looking at
educational software for use in the biology classes here at UW.  The
group is composed of several graduate students and PhDs from the
Department of Zoology at the UW.  In addition to gathering software, we
have run classes here examining biology education software, have
invited notable people in the field to come and speak at our
departmental seminars, and some of us are authors of educational and
other software.  Among the primary people involved in the group are
Adrian Sun, George Gilchrist, Tarif Awad, Creagh Bruener, David
Baldwin,  Kevin Obrien, and Eli Meir (the author of this FAQ).  

We are not claiming to be especially knowledgable or gifted when it
comes to educational software, nor are we claiming to be teachers who
are speaking from years of experience in using computers in education. 
We have provided some references to articles and reviews by people who
are much more knowledgable than we are.  Rather, based on our
experience as students, teachers, and authors of materials for
undergraduate education, we aim to present what we think are the most
useful pieces of software for undergraduate education in various
branches of biology.  We hope this will provide a starting point for
instructors in other universities who are looking for good software to
use in their classes.

(1b)  Where to address comments, queries, etc..
You can get in touch with us by emailing to
best at, or by emailing the author of this document
at meir at  You can also get us through snail mail
by sending to 
Eli Meir
Dept. of Zoology, NJ-15
University of Washington
Seattle, WA 98195

(1c)  How we picked software to include here

In searching for educational software, we quickly realized that there
is lot of stuff out there which is not very interesting.  We did not
want to include all of that in our list, so we have weeded out a lot of
software.  This weeding is obviously subjective.  What one person
considers junk might be exactly what another person is interested in. 
Originally I was going to spell out these biases in this FAQ, but due
to lack of time, here is a quick summary.

First of all, anything that did not work on a reasonably new computer
and operating system was excluded.  We also excluded most software
which did not run on a Macintosh or IBM machine, since that is what
most students and teachers have access to.  There is some bias towards
Macintosh software, since that is the computer which most of us have
sitting on our desks, but we included any good IBM software we came
across as well, and have also included a small amount of UNIX software.

Secondly, we have a bias against software which puts a textbook or a
study guide onto the computer and claims that just the fact its on a
computer screen makes it somehow superior.  We also did not
particularly like most software whose only innovation was a bit of
hypertext capability (ie - click on a word, it gives you a definition
of the word or takes you somewhere else in the document).  We do like
software that uses the computer to do things which would be hard or
impossible to do on paper.  We especially like simulations and other
programs which let a student perform experiments.

(1d)  What information we include about each piece of software we

We have tried to write three paragraphs about each piece of software we
have seen.  The first paragraph gives our description of what the
software does.  The second paragraph is a short review of the software.
 The third paragraph gives information on how to get the software, and
approximate price range if we know it.  In the price range, Free means
free, Low means $100 or less, and High means more than $100.  These are
by no means gauranteed to be accurate.

We have NOT class tested most of this software, so the reviews are
based on our impressions as students and teachers.  In general, only
one or two people have looked at each piece of software, and most
titles have only been looked at by the author of this FAQ.  Because of
this lack of class testing and the small number of reviewers, we have
limited each review to a single short paragraph which states what we
see as the strengths and weaknesses of the package, and our gut feeling
about how useful we think it is.  We hope that this short review will
help users of this document to decide what software they are
interesting in looking for on their own, but do not intend it as an
authoritative statement on the value of the software.  Also note that
we have in essence given favorable reviews to all software included
here, since quite a bit of software was left off this list (well over
50% of what we looked at is not on here).

If someone other than the author of this FAQ contributed to a review,
their initials are given next to the software title.

(1e)  How to submit software for inclusion on this list

We welcome new software, and will be happy to include it in the list if
it meets our criteria as discussed above in (1c).  However, there are a
couple conditions.

(I)  We will only accept software for review from the authors or
publishers of the software, or on an original store-bought disk with
the manual.  This does not mean that others cannot tell us about
software they have used and liked.  We really want to hear about
software from everyone, and if you inform us of a piece of software and
tell us how to get ahold of it, we will do our best to get a copy and
look at it.  However, to protect us from copyright problems, virus
problems, etc., we would rather only receive software from the actual
authors, or from anonymous ftp sites if the software is in the public
domain.  When cost is a factor, we may review demo versions of software
instead of the full package.

(II)  We prefer reviewing real copies of a piece of software, rather
than a demo version, and if we have only seen a demo version then we
will mention this in our review.

(III)  We prefer receiving software on a diskette.  We also would like
to see a manual, or any other documentation which exists.  The
documentation can be included as a file on the disk, if you prefer, in
either ASCII, Microsoft Word, or Wordperfect formats (UNIX software can
have documentation in standard unix formats).  If you want to send
software to us via the network, please inform us beforehand that you
plan to send us something.  For our protection, we may still request
something in writing stating that you are the author (or at least a
phone number).

(IV)  We would also welcome contributions from people outside the group
here at UW.  If you would like to submit a review for this FAQ, please
write it in the form of the other descriptions here, and send it to us
with some indication of how you have used the software and what your
qualification is to review it (it does not have to be very high, but we
would like to know).  If we are satisfied that it is a fair description
of the program, then we will include it in the next release of the FAQ.
 We will also try to get ahold of a copy of the program ourselves to
look at.

(2)  Resources for information on biology education software

(2a)  BioQuest

This is a consortium of software developers and educators which have
gotten together to produce a CD full of really good biology education
software.  Many of their programs are described in this document, and
you can get fuller descriptions of their programs by getting their
Intro_to_BioQuest hypercard stack off of the internet.  Before putting
a piece of software on their CD, they subject it to a pretty rigorous
peer review process, and make sure its been tested in many classrooms. 
I think that this is some of the best stuff out there, and well worth
the price (which is quite cheap - under $100 last time I checked for
all of their programs for a single user, more expensive for a site

In addition to software, the BioQuest group has developed a whole
philosophy of education, which they use to guide their development and
selection of educational software.  This philosophy revolves around the
three Ps - Problem-posing, Problem-solving, and peer-Pursuasion.  They
describe this philosophy better than I can here, so I will let you get
ahold of it yourself.  It is well worth reading their material, even if
you do not end up using their software.

To get the Intro_to_BioQuest hypercard stack, look
of in one of the macintosh anonymous ftp sites (info_mac, etc.).

To order the BioQuest CD, send email to asdg at, or write to
		Academic Software Development Group
		Computer Science Center
		University of Maryland
		College Park, MD 20742
For information, you can write to BioQuest at

(2b)  CTI Centre for Biology

This is a gopher site which you can access with mosaic that includes
reviews of some 650 pieces of software for teaching biology.  The
reviews are pretty short, saying the name of the software, the
distrributor, what types of computer it works on, and giving a short
paragraph of description.  There is also a warning at the beginning
that the information has not been kept up to date since 1991, although
there are reviews of software that have come out since then.  The big
advantage to this database is that it is the most comprehensive of any
we have seen - over 650 products are listed - so it might be a good
place to start a search.

Get there using Mosaic -

(2c)  NECUSE Biology Software Reviews

This is a book of biology software descriptions and reviews, with more
information than what is included here.  The 1994 version covers almost
50 titles.  The reviews are organized by topic, with various indexes in
the back.  Along with information such as author, supplier, cost,
computer system, etc., is a short description of the program, a set of
poor/good/excellent grades for a number of criteria, and a synopsis of
the programs strengths and weaknesses.  There is also an extensive list
of videodisks in the back, with just one line of description and a
price and supplier.

To get this book, write to Carol Ann Paul at Wellesley College, or
Graham Kent at Smith College (Dept. of Biological Sciences, Smith
College, Northampton, MA 01063).

(2d)  Quarterly Review of Biology

The Quarterly Review of Biology is one of the few sources for academic
reviews of software interesting to biologists.  Each issue includes a
few software reviews, not all of educational software, but quite a few
are.  The reviews are generally written by an expert in the field, and
are pretty good (much more thorough than those here).

(3)  Ecology and Evolution Software

(3a)  Biota

This program lets you play around with differential equation models in
ecology.  It is very different, however, than some of the other ecology
programs listed here in that it lets you mix and match classical
ecological equations with each other to make systems of equations. 
This works as follows.  You can have up to 10 different species and/or
ecosystem components.  Each species has an equation which governs its
growth and death, for instance exponential, logistic, lotka-volterra,
and so on.  You may also add in interactions between the species, such
as specifying one of the species as a predator on another one, again
governed by classical differential or differencce equations.  Each
equation has a set of parameters that you can set.  You then run the
models and watch population sizes over time of each species.  You can
also sample the populations using a couple of sampling techniques, and
you can specify that the sampling include error to simulate real life

In addition, the program lets you add in a spatial component to the
models, by having separate populations of each species in distinct
spatial areas.  You can have up to 200+ spatial areas, and in each one
you can independently specify starting conditions.  You can then
specify how migration will occur between each pair of cells for each
species cells.  The program will give you separate population size
graphs for each area when you run the model, so you can look at
metapopulation dynamics, island biogeography, etc..

The user interface for Biota is particularly well-designed, given the
complexity of the program, and lets you easily change equations and
parameters through pop-up menus, dialogs, and maps of the different
areas.  Because of the ability to mix and match equations, species, and
areas, you should be able to use this program to design and play with
models demonstrating many concepts, from simple population growth
models to moresophisticated concepts involving space and several
interacting species.  Nevertheless, I would be hesitant to use this in
an introductory class, because despite the nice user interface the
level of understanding you need to figure out what is going on is still
fairly high.  There are a lot of equations and interactions to keep
track of, and you need to understand these at least superficially to be
able to play with parameters, and interpret the graphs of population
size in light of those parameters.  Building new models that are stable
is also not trivial.  So I think this program would best be used in
more advanced ecology courses, where either you want students to be
able to play with models but do not want to use a full-blown modelling
program such as Stella or Mathematica, or you want to be able to play
with spatially-explicit models.

Computer:  Macintosh

Source:  BioQuest     asdg at    or see address above under

Cost:  Low (single user) / High (site license)

(3b)  Environmental Decision Making

These are a series of three modules built around a crippled version of
a program called Extend.  Extend seems to be a program somewhat like
Stella (see review).  Using the version of Extend included, you can run
three different models, one of a grasslands ecosystems with fires, a
second looking at logging, and a third looking at fishing.  Each model
has functional blocks representing things like trees, fire, logging
effort, and cash.  You are asked to connect the blocks together to make
ecosystems, and then to connect these ecosystems to human management
systems.  The manual takes you through this process step-by-step.  You
can then play with changing selected parameters of each block, and
running the model to see what happens to population sizes (or the
equivelant variable) in each component of the system over time.  The
authors of these models want students to focus on the process of model
building, and how you calibrate and use models, rather than on the
models themselves, so all the parameters for each block are easily
available to be played with, and the equations connecting the blocks
are not shown from within the program.

The models which the authors have developed are nice, and should be
useful in a course looking at the interactions between people and
ecosystems.  The software makes it fairly easy to change parameters and
add and remove links between things, though there are a lot of
extraneous tools and commands that could potentially confuse
non-computer literate students.  However, in more than an introductory
class, or if the instructor would like to modify these models instead
of using them as is, then I think it would be better to go with a
full-blown modelling program such as Stella, or perhaps the full
version of Extend.

Computer:  Macintosh

Source:  BioQuest     asdg at    or see address above under

Cost:  Low (single user) / High (site license)

(3c)  Evolve

This is a population genetics simulator.  It simulates evolution in a
two-allele system, with natural selection, genetic drift, and gene
flow.  You can set separate survival and reproductive rates for each
genotype per generation, number of immigrants of each genotype,
percentage of each genotype which emigrates,  and to simulate
evolutionary bottlenecks and genetic drift you can set a maximum
population size, after which the population crashes down to a lower
population size (by randomly killing individuals of all genotypes). 
You can also use one set of parameters for a certain number of
generations, then change the parameters and continue running the model,
simulating environmental variability.  The main interface to the
program is a graph window where you can choose to plot the frequencies
of each of the genotypes in the population, the allele frequencies, the
population sizes of each genotype, and/or the total population size. 
All of these results and more are also shown in a table at the bottom
of the window.  To facilitate comparisons between the results from
different parameters settings, you can run multiple trials and plot one
trial on top of another.  All the parameters are set within a single
dialog box.

This program is quite nicely laid out, with a lot of information and
controls put into a single window and a single dialog box in a way that
makes them both easy to access and not too confusing.  I expect that
students would need a few minutes to figure out the what they were
looking at, but once you get comfortable with it then the program is
very easy to use.  The program is flexible enough to do a most
evolution experiments you could think of doing with a two alleles at a
single locus.  The manual is clear and well written, and includes
exercises to get students started.  This program should be useful from
introductory through advanced undergraduate genetics and evolution
courses, especially in courses which plan to make somewhat extensive
use of computer simulations (say more than one or two hours).

Computer:  Macintosh

Source:  BioQuest     asdg at    or see address above under

Cost:  Low (single user) / High (site license)

(3d)	PopGen / Simul8

These are simple population genetics simulations, one for the macintosh
(PopGen) and the other for DOS or UNIX.  In PopGen there are two modes,
one a simulation of evolution at a single locus, and one a quantitative
simulation mode.  In each mode, the program puts up two windows, one
containing a graph and the other with a series of slide bars
controlling the parameters of the model.  For the single locus mode,
the graph shows the percentage of the alleles which are of type A
(there are only two alleles) over time.  Parameters include the size of
the starting population, the initial percentage of A alleles, the
selective fitness of each allele combination, the mutation rates
between alleles, and various types of migration between populations (up
to eight populations can be run simultaneously).  The quantitative mode
shows the changes in mean values of two quantitative characters over
time, also with a set of parameters that you can change.  Simul8 (the
DOS/UNIX version) is similar but does not include the quantitative
mode, and uses a character menu to change parameter values instead of
sliders (ie. type 1 to change size of starting population, etc.).

Both versions are simple and straightforward to use.  The only
complaints I had were that the slide bars in PopGen are a little
clumsier than most macintosh slide bars, and the parameters are
sometimes not erased and redrawn properly.  The character menu in
Simul8 may take a moments explanation for students who started with
computers after that style of interface become obsolete, but should
pose no real problems.  You should also know some population genetics
before sitting down with this program, as there is no help onscreen and
the manual is very short and does not provide any sort of tutorial. 
But these are not fatal flaws, and this program should be quite useful
for students to play with these simple population genetics models and
see how changing different parameters changes the outcome.  You might
also look at Evolve, which has similar goals but is a little more
extensive (though it does not include the quantitative mode).

Computer:  Macintosh (PopGen),  DOS (Simul8)

Source: (,  in 

Cost:  Free

(3e)  Blind Watchmaker

This is an implementation of the program Richard Dawkins used in
writing his book of the same name.  The screen displays a population of
tree-like stick figures, each figure drawn according to a genetic code
of parameters.  Parameters are such things as the number of branch
points, the length ratio between the larger and smaller branches,
whether the figure is symetric or asymetric, the angles between
branches, and so on - about 16 all together.  The figures evolve
through artificial selection, meaning you are presented with a series
of figures on the screen which are all slightly different from each
other, and you select which one you want to breed to make the next
population.  You can also ask the computer to drift through parameter
space, showing a little movie of different shapes as it goes, or you
can search the space more methodically.

Using this program you get a nice demonstration of how evolution can
generate fairly complex shapes from pretty simple beginnings, and how
selection can bring this about.  The user interface is easy to figure
out.  The program seems to have a little trouble with newer computers. 
You can run it, but you cannot multitask.  However, we have an old
version of the program, so perhaps this has been fixed.

Computer:  Macintosh

Source:  W. W. Norton & Company, NY

Cost:  Low

(3f)  Environmental Science Stella Stacks

This is a series of simple programs which cover a variety of topics in
environmental science.  The individual programs are titled Energy Flow,
Carbon Cycle, Ozone Depletion, Island Biogeography, Population
Momentum, Max. Sustainable Yield, and Rock Cycle.  What each program
does is described below.  All the modules are simulations, with the
user interface done through hypercard.  For those of you unfamiliar
with hypercard, its an interface which is designed to look like a
series of index cards, where you flip from one card to the next to get
from one topic to the next.  Each module lets you set one or more
variables of the simulation (using sliders which you move with the
mouse), run it, and then look at the results either as a table or on
graphs.  In some of the simulations you are asked to predict what the
output graph will look like before you actually run it.  There is a
minimal amount of text explaining each model, along with some cute
sound effects and speech which hilight some actions.  The simulations
were all written in Stella (see the entry on Stella below), and each
module lets you look at a schematic of its model.

In general, these are quite nicely done programs.  The user interface
is quite simple and consistent across all modules, although because its
done in Hypercard there is a lot of flipping back and forth from one
screen to another.  The text on screen is enough to guide most students
through the simulation, though there is very little background material
in most of the modules.  A very nice feature of some of the modules is
that they ask the student to predict what will happen before running
the model, and then superimpose the real results on top of the
predictions.  These programs would all work well as 1 hour computer
labs or in discussion sections in an introductor ecology or
environmental science course.  They are too simple to be used for more
extensive labs.  Individual descriptions and reviews follow.

The Energy Flow module puts the student in charge of managing the
Silver Springs Ecosystem, which consists of producers, herbivores,
predators, decomposers, and top predators.  As a manager, you control
the number of tourists coming through the system, which controls how
many bread crumbs get fed to the herbivores, and so controls the energy
flow through the whole system.  Your job is to keep exactly 10 top
predators around for five years, and especially not to let top
predators get too low or too high, by regulating the flow of tourists. 
The aim of the module is to demonstrate that management is hard,
especially when there are time lags between the input that you control
(bread crumbs) and the output that you desire (10 top predators).  The
program serves this purpose, although it wonÕt take too long for an
observant student to get it right.

Th Carbon Cycle module demonstrates the basic parts of the global
carbon cycle.  The model includes burning fossil fuels, decomposing of
organic matter, respiration, net destruction of vegetation, and carbon
escaping from the oceans as source of carbon and gross primary
productivity and the oceans as sinks.  You are shown a schematic of all
these sources and sinks, and clicking on any one of them will bring up
a short explanation of its role.  The student is given the mission of
keeping global atmospheric carbon dioxide below 720 e15 grams, by
adjusting each of the sinks and sources.  After running the model and
comparing the results to your predictions, you can get explanations of
some of the features of the results such as why there are yearly
oscillations in the carbon cycle and the effects of the different
sources and sinks.  This module works nicely as a simple introduction
to the sources and sinks of carbon dioxide in the world, and their
relative magnitudes.  It is also a nice introduction to how modelling
of this sort is done. Since these C02 models are in the news a lot as
part of the debate on the greenhouse effect,  the content of the
program should be interesting to students in a variety of introductory
classes.  I see a potential problem, however, if the teacher does not
make it clear that this is only a caricature of how the real world
works (especially since the model is so simple, and does not include
connections even between the variables which exist such as vegetation
destruction and GPP), and would also want to make clear that while you
can change things in the model such as CO2 flux into and out of the
oceans, GPP, etc., in real life there are no slide bars on these
things.  Still, if the teacher makes these points, the program should
serve as a good integrater and solidifier of both how a nutrient cycles
on a global basis, and some of the variables involved in the debate on
the greenhouse effect.

The Island Biogeography module is a simple demonstration of the theory
of island biogeography.  It gives a short introduction to the theory
with the requisite three graphs showing effects of distance from
mainland and size of islands, then lets the student play with a simple
model of species colonization and extinction, where you can adjust the
distance of an island from the mainland and the size of the island, let
the model run for some preset amount of time, then look at graphs of
number of species, colonization, extinction and turnover rates over
time.  At the end are a series of questions about the results from the
model, with the option to go back and rerun the model to check your

The Population Momentum module explores how the worlds human population
grows. After a short introduction on population growth and U.N.
predictions of this growth, theprogram presents you with a model of an
age-structured population.  The population has 11 categories, including
three pre-reproductive ages, four reproductive ages, and four
post-reproductive ages.  You can set the number of individuals in each
class, and an overall reproductive rate for the population.  As you run
the model the population structure is shown changing in a horizontal
bar graph (the classical representation of population structure).  At
the end are several questions about the results of the model, with the
option of going back and rerunning the simulation to answer them.  The
thrust of the introductory text and the questions is that even with
just a replacement rate of 
reproduction, the human population can grow quite a bit before reaching
equilibrium.  Look at BioQUESTÕs Demography for another program with
the same idea but a somewhat more flexible model.

The Max. Sustainable Yield module lets students try to harvest fish
using two different harvesting strategies, fixed quotas, and variable
effort, using a very simplistic model.  There are several screens of
introductory material which discuss fixed quota and variable effort
harvesting strategies, using graphs of population size vs. recruitment
to show how each of these work.  You can then try each of these
strategies out on a model of a fish population.  The model is of
logistic growth, with the parameters of the growth fixed.  Before
running the model, you can set the initial population size, and either
the amount harvested per year (fixed quota) or the rate of harvesting
(variable effort).  When you are done playing with the model, the
program asks you several questions about the resource management
strategies you just played with.  This program would work best after
students have been introduced to some theory on population growth (ie.
what a population size vs. recruitment rate graph shows) and harvesting
strategies.  Even then, a problem with this program is that the model
has no probabalistic elements in it, and so if you pick the right
values, both harvesting strategies work just as well.  Without chance,
you have to play around and imagine for yourself that chance was acting
to see the greater risk inherant in harvesting by quota than by a
variable effort strategy.  There is also no graph of amount harvested
per year, so you cannot look at how efficient your harvesting strategy
is.  However, the program works as a very basic introduction to these

The Ozone Depletion and Rock Cycle  modules are similar to the others,
but since they are only peripherally concerned with biology I do not
review them here.

Computer:  Macintosh, also needs Hypercard 2.2 or higher (will not work
with Hypercard player).

Source:  Wm. C. Brown, Publishers, Business and Educational
Technologies, 2460 Kerper Boulevard, P.O. Box 539, Dubuque, Iowa,
52004-0539.  1-800-258-2371.

Cost:  High (plus cost of Hypercard from Apple).

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