Biology Education Software FAQ (1 of 3)

Eli Meir meir at zoology.washington.edu
Tue May 30 14:23:57 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)  WhatÕs 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
review
	(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
	(3e)	Energy Flow Stella Stack
	(3f)	Island Biogeography StellaStack
	(3g)	Max. Sustainable Yield Stella Stack
	(3h)	Carbon Cycle Stella Stack
	(3i)	Population Momentum Stella Stack
	(3j)	Blind Watchmaker
	(3k)	Simlife
	(3l)	Populus
	(3m)	PopDyn
	(3n)	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)	NeuroLab
	(4g)	SymBioSys
	(4h)	Quantitative Circulatory Physiology

(5)  Cell and Molecular Biology
	(5a)	Genetics Construction Kit
	(5b)	SequenceIt!
	(5c)	PurifyIt!
	(5d)	RateIt!
	(5e)	Enzyme
	(5f)	MacMolecule
	(5g)	Visual Genetics
	(5h)	Virtual Genetics Laboratory
	(5i)	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 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.  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 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 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 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 for a single user, more expensive for a site
license).

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:
	http://www.biology.iupui.edu/BioQUEST/./
of in one of the macintosh anonymous ftp sites (info_mac, etc.).

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 - http://www.liv.ac.uk/ctibiol.html

(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.




(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
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 (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 umdd.umd.edu    or see address above under
Resources.

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 umdd.umd.edu    or see address above under
Resources.

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


(3d)	PopGen

This is a simple population genetics simulation.  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.

This program is simple and straightforward to use.  The only complaints
I had were that the slide bars are a little clumsier than most
macintosh slide bars, and the parameters are sometimes not erased and
redrawn properly.  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 doesnÕt 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 doesnÕt include the quantitative mode).

Computer:  Macintosh

Source:  evolution.genetics.washington.edu (128.95.12.41),  in 
/pub/popgen

Cost:  Free


(3e)  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

(3f)  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





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