Proposed Bio Educ Software FAQ (long) (2 of 3)

Eli Meir meir at zoology.washington.edu
Fri Mar 24 01:18:00 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


(1)  WhatÕs in this FAQ?
      (a)  Who is B.E.S.T. ?
      (b)  Where to address comments, queries, etc..
      (c)  How we picked software to include here

(2)  Resources for information on biology education software
      (a)  BioQuest
      (b)  
      (c)  References

(3)  Ecology and Evolution Software
      (a)  

(4)  Physiology and Neurobiology

(5)  Cell and Molecular Biology

(6)  General purpose software useful in education

(7)  Collections of pictures, facts, etc..

(8)  Textbooks on CD


(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 PhDÕs 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.

(1b)  Where to address comments, queries, etc..
You can get in touch with us by emailing to
best at zoology.washington.edu, or by emailing the author of this document
at meir at zoology.washington.edu.  You can also get us through snail mail
by sending to 
Eli Meir
B.E.S.T.
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, hereÕs a quick summary.

First of all, anything that didnÕt work on a reasonably new computer
and operating system was excluded.  We also excluded most software
which didnÕt 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
review

We have tried to write three paragraphs about each piece of software
weÕve 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 many
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).

(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.  This does not mean that others cannot tell
us about software theyÕve 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 doesnÕt have to be very high, but
weÕd like to know).  If we are satisfied that it is a fair description
of the program, then weÕll 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).

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 PÕs - Problem-posing, Problem-solving, and peer-Pursuasion.  They
describe this philosophy better than I can here, so IÕll let you get
ahold of it yourself.  ItÕs well worth reading their material, even if
you donÕt end up using their software.

To get the Intro_to_BioQuest hypercard stack, look in one of the
following url locations or ftp sites:


To order the BioQuest CD, send email to asdg at umdd.umd.edu, 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 beloit.edu

(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
weÕve seen - over 650 products are listed - so it might be a good place
to start a search.

Get there using Mosaic - its at Liverpool University Computer Science
gopher site in the UK.

(2c)  NECUSE Biology Software Reviews

This is a book of biology software descriptions and reviews, with more
information than whatÕs 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.


(2e)  Starting World Wide Web Sites

There are whole usenet groups devoted to biology stuff on the world
wide web, so IÕm not going to cover that here.  However, IÕll just list
a few sites which can lead you to more information.



(3)  Ecology and Evolution Software


(3c)  Energy Flow Stella Stack

This program puts you in charge of managing Silver Springs, an
ecosystem which includes primary producers, herbivores, predators, top
predators and decomposers, as well as tourists which throw scraps of
bread to the herbivores.  Your job is to keep the population of top
predators at a certain value for 5 years, by regulating the number of
tourists who are allowed in per year.  You are first introduced to the
model by watching it get built on the screen.  You are then told your
goal of regulating top predators, and asked to make a predication about
the population size of the top predators over the next five years (you
both draw a graph of what you think population size / time will look
like, and write down how you intend to accomplish this).  You can
adjust the starting populations of each component in the ecosystem, and
the number of tourists.  As the model runs, it gives you feedback about
how well youÕre doing, and you can continually adjust the number of
tourists to try to regulate the population.  At the end, you get plots
of population size over time for each component of the model, and the
top predator plot is overlayed on your prediction, so you can see both
how well you did and how well you predicted what would happen.  

This program was designed to be simple to use, and takes students
step-by step through the exercise.  It shares a common interface with
all of KeslerÕs programs (see Enzyme Kinetics for a more complete
description).  It has the problem of running a little too fast on a
fast computer, but other than that works quite well.  The exercise is a
little simplistic, and will not challenge more advanced students. 
However, for introductory ecology or conservation biology classes, this
program should be quite useful, and should easily work in a one hour
lab or discussion period.

Computer:  Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).

Source:  David Kesler, Rhodes College.   email:  KESLER at ns.rhodes.edu

Cost:  Free

(3d)  Island Biogeography StellaStack

This 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 answers.

This program is very simple to use, and takes you step-by-step through
the whole exercise.  It shares a common interface with all of KeslerÕs
programs (see Enzyme Kinetics for a more complete description).  The
program does not contain a full description of island biogeography and
its implications, and so would be most useful as a supplement to a
lecture or reading on the topic.  In addition, it is very simplistic,
and would not be useful as more than a reinforcement of the concept.
for introductory students.

Computer:  Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).

Source:  David Kesler, Rhodes College.   email:  KESLER at ns.rhodes.edu

Cost:  Free

(3e)  Max. Sustainable Yield Stella Stack

This program 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).  You are
asked to make a graphical prediction of the population size over time,
given your initial conditions.  After running the model, you can see
the simulated population size over time superimposed on top of your
prediction.  When you are done playing with the model, you can read
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.  The program
itself is simple to use, and shares a common interface with KeslerÕs
other programs (see Enzyme Kinetics for a description).  One 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 concepts, and may be useful in
introductory ecology or conservation biology classes which discuss
management.

Computer:  Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).

Source:  David Kesler, Rhodes College.   email:  KESLER at ns.rhodes.edu

Cost:  Free

(3f)  Carbon Cycle Stella Stack

This program demonstrates the basic parts of the global carbon cycle
through the use of a simple model.  The model includes five sources,
and two sinks of carbon.  The sources are burning fossil fuels,
decomposing of organic matter, respiration, net destruction of
vegetation, and carbon escaping from the oceans.  The sinks are gross
primary productivity and the oceans.  The student is introduced to
these through a picture of all the sources and sinks, with small
explanations of each.  The student is given the mission of keeping
global atmospheric carbon dioxide below 720 e15 grams, by adjusting
each of the sinks and sources.  Before running the model, you are asked
to make a graphical description of what you think the CO2 level will be
over the 5 years that the model is run.  You can then run the model,
and at the end of each run look at a graph of the CO2 level over time
in the simulation, and see how this compares to your prediction.  There
are also a series of short explanation of the effects of changing each
of the variables.

This program 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. 
The user is guided through the steps in the exercise using an easy to
understand interface that is the same as that in KeslerÕs other
programs (see Enzyme kinetics for description).  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
doesnÕt 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.

Computer:  Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).

Source:  David Kesler, Rhodes College.   email:  KESLER at ns.rhodes.edu

Cost:  Free

(3g)  Population Momentum Stella Stack

This program explores how the worldÕs human population grows.  After a
short introduction on population growth and U.N. predictions of this
growth, the program 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.  You are
asked to predict how the population will grow over time by drawing a
graph of this growth, which you can then compare to the output you get
after running the model.  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.

The program is very simple to use, and takes you step-by-step through
the exercise.  The interface is similar to the other programs by this
author (see Enzyme Kinetics for a description), and works well.  This
program would make a good one hour lab in an introductory course which
talks about human population growth.  You may, however, want to look at
the BioQuest program Demography (see description above), which is a
more flexible program also looking at human population dynamics.


Computer:  Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).

Source:  David Kesler, Rhodes College.   email:  KESLER at ns.rhodes.edu

Cost:  Free

(3h)  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
sampling.

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 whatÕs going 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 donÕt 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 umdd.umd.edu    or see address above under
Resources.

Cost:  Low

(3g)  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 umdd.umd.edu    or see address above under
Resources.

Cost:  Low

(3h)  Evolve

Computer:  Macintosh

Source:  BioQuest     asdg at umdd.umd.edu    or see address above under
Resources.

Cost:  Low


(3i)  Blind Watchmaker

This is an implementation of the program Richard DawkinÕs 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 Ôgenetic
codeÕ 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 ÔdriftÕ 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 canÕt 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



(3j)  Simlife

This is a commercial game, put out by the same people that did SimCity,
SimAnt, SimEarth, and more.  The idea is to build an ecosystem, by
designing animals and plants to put into it and then letting them run
around have sex, die, etc., with evolution and mucking around from god
(you).  Being a commercial program, its very slick, with nice graphics
and animation, sound effects, full color maps of the game world, and a
well-written manual.  To make a creature, you give it a number of
attributes such as what types of food it eats, how it moves (swim, fly,
walk), what type of movement pattern it has, how long it takes to reach
maturity and start having kids, and many, many more (probably over 50
characteristics total, many of them continuously variable).  You also
have some control over weather, the terrain in your world, how quickly
evolution happens, and other factors.

SimLife is a really fun game, you could easily spend hours playing it. 
That said, its probably not too useful as a biology teaching tool,
especially at the college level.  When the game first came out, there
were several discussions on the net about its utility as a teaching
tool, and for the most part people gave it reserved praise at best. 
Still, it might be worth looking at.  If nothing else, its a good way
to procrastinate, and its better for your students than television.

Computer:  Macintosh

Source:  Any mail-order company

Cost:  Low

(3k)  Populus


(3l)  PopDyn

(3m)  Fish Farm

This program puts you in charge of raising fish in a pond.  You are the
manager of the farm, and you need to figure out how best to raise the
fish to maximize your profit.  You can control a variety of factors
including how densely you initially stock the fish, how much protein
you put in the fish food, the rate at which you turn over the water,
how much you aerate the water, and so on.  Your job is to experiment
with these different variables to find the optimal way to raise fish in
your farm.  The program lets you change each variable separately, make
a run with that setting, and then gives you a summary of how you did in
that run.  As the model runs, it shows you various statistics on the
screen telling you how well youÕre doing.  The program will also take
the data from several experiments and make graphs of profit versus
different values of one of the variables.

This program is quite engaging, and really makes you think about how to
go about finding out an answer to a question which depends on many
variables.  For instance, you will have trouble finding the optimal
fish growing method if you donÕt change one variable at a time.  The
user interface is quite clear and easy to use.  Everything is done
through buttons and dialog boxes where you can type in numbers, and all
the information you need is on the screen.  The one annoying thing
about the interface is that to go from one experiment to the next you
must traverse four or five dialog boxes which gets tiresome after a
while.  However, other than that minor complaint, this program is quite
nice.

Computer:  Macintosh

Source:  Benjamin/Cummings Publishing Company, ??

Cost:  Low?

(3n)	MacClade

Computer:  Macintosh

Source:  Sinauer and Associates, ??

Cost:  Low?


Eli Meir
Dept of Zoology, Univ of Washington
meir at zoology.washington.edu




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