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A few reviews on biology-ecology related software tools.
[log in to unmask] does not endorse the use of any of
the software packages listed herein unless they are
free/shareware or self cost applications developed by scientists
for scientists. Cheers, APS.
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Dobson,Alan (1988): Acid-Base Simulation. (Wisc-Ware) [BIOLOGY,
CHEMISTRY, DOS<This program is the best I have ever seen in the
sense of simplicity. There are two commands that I have not seen
in any other program - the first one is called control guided
tour and the second is called the menu guided tour. The first
shows automatically how to perform a simulation using the hints
s/he has in the program, and the other one shows a person who is
unfamiliar in using windows or a mouse how to do so. For
example, it demonstrates how to change the size of the window or
how to close a window, etc. Because of these two commands, I
think there is no need for a teacher to show you how to use this
program. I did know how to perform a simulation, but when I used
the control guided tour it showed me exactly how to do so. I
strongly recommend this program for in class use by students of
any classification. However, like the author said the student
should be familiar with the respiratory and the renal function.
Note: In my opinion every program should have at least the
control tour guide so that if somebody has difficulty using the
program, s/he would not waste so much time getting familiar with
the program if such commands existed. (REVIEW 1: RATING = 9)
This program was really easy to use. The fact that it is used
under windows with a mouse makes all the commands easily
accessible. I thought the experiment was neat and it did a good
job of demonstrating equations and graphs. I really like the
control guided tour. These options allowed me as a naive user to
view different controls and there functions. This feature really
helps the user be aware of and take advantage of every option the
software has. I think that the format of the software could be
applied to other programs in order to make them easier to use.
In my opinion, this program could be used successfully by all
students. (REVIEW 2: RATING = 8)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Will,Ed (1987): ANIMAL KINGDOM. (Hypercard application)
[BIOLOGY, MAC, TAXONOMY <This program is a very small program
that would have very limited use. The basic uses that I could
see include a basic animal kingdom class to see how the taxonomic
structure is developed. The program itself is not very friendly.
The user must know fully how to use HyperCard on the Mac. Even
then, the program is not well labeled. There doesn't seem to be
much extended use for this program. (REVIEW 3: RATING = 4)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Jeanne,Robert (1988): Ants. (Wisc-Ware) [BIOLOGY, DOS-WINDOWS]
<Ants is an interactive program to study the system reliability
of different ant foraging strategies. In this program you are
asked to select a particular strategy and input the necessary
information for that strategy. A schematic for the strategy is
either drawn automatically or you are given the opportunity to
design one yourself. After the schematic has been drawn the
graph of the strategy may be displayed. This plots individual
reliability versus system reliability. A max of five plots may
appear on the graph, after that the oldest one will be replaced
by the new one. The program is easy to use, but for better
understanding of the program you should be familiar with ant
foraging and reliability theory. The author suggests the reading
of the following paper: Joan Herber, "Reliability Theory and
Foraging by Ants", J.Theor. Bio., 1981, 89:175-189. The program
requires Windows to run. You cannot save a certain schematic for
a strategy you have chosen, also you cannot print out a graph or
a schematic figure for the strategy you have chosen or clear a
graph from a window. (REVIEW 1: RATING = 4)
This is very specific software that was designed specifically to
study the foraging strategies of ants. The software is very user
friendly in the fact that it is used under Windows and the
commands are really easy to understand. I had no problem using
the program, and I think that even people with very limited
computer knowledge could use it. However, the program does
require previous knowledge of the subject matter. This limits
the use of the program because it cannot be used as a teaching
device. The program can only be used to demonstrate specific
examples and supplement what has already been learned. The
program also has no way to clear graphs, therefore the user must
continually look at five graphs and try to figure out which is
the most recent. This could present a problem especially if the
graphs vary by only a small amount. Also, there is no way to
save situations you create or print graphs. I thought the
program would have been a lot more useful if there were examples
already loaded onto the system that you could experiment with.
The thing I liked the best about the program is the you can
design your own schematic- this was easy to do and made the
program interesting. In my opinion, this software would be a lot
more useful if explained the subject matter as well as gave
examples. (REVIEW 2: RATING = 4)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Camazine,Scott (1990): Automata. (Cornell University, Section of
Neurobiology and Behavior) [CHAOS, MAC<This package includes a
number of files of different chaos images. The package also
contains a program that will create random images. This could be
useful for pattern analysis. I am not sure of what the
applications of this program will be, but it has some nice
features and good graphics. (REVIEW 3: RATING 7)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Macey,Robert I; Calley,John N; Curylo,Alex T (1991): Axon.
(BioQUEST) [ECOLOGY, MAC <A simulation of the classic
Hodgkin-Huxley (1952) model for axon excitation formulated from
their voltage clamp measurements upon the squid Axon. It
provides you with a simulated excised peripheral nerve from a
squid and allows you to perform experiments by setting the
environment of axon and stimuli or clamps applied to it and view
graphically assorted nerve properties, such as threshold,
refractory period, accommodation and summation.>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Frischknecht,Markus (19--): BIO-ESS. (University of Berne,
Institute of Zoology, Wohlenstrasse 50a, Switzerland, e-mail:
[log in to unmask]) [ECOLOGY, MAC <This is a stack that
demonstrates some aspects of evolutionary stable strategies. The
Hawk and the Dove have different strategies in a population model
in which species fight each other to get a resource. Each time a
Hawk meets another Hawk they start risky fight. The probability
to win is 50%. The probability to meet another Hawk is the
frequency of this strategy in the population. But if the
competitor is a Dove then the Hawk gets all the resource. When
two Doves meet they share the resource. The game is fun, it is
user friendly and has option to change the model which calculates
the frequencies. Graphics are nice. And the author states all
the limitations such as the variable "value" and "damage" should
not exceed 10 because the frequency becomes negative which makes
no sense, etc. (REVIEW 2: RATING = 7)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Odell,Garrett M; Segel,Lee A (1987): Biograph. (Cambridge New
York New Rochelle Melbourne Sydney) [CALCULUS, DIFFERENCE
EQUATIONS, DIFFERENTIAL EQUATIONS, ECOLOGY, MODELING, DOS]
<Biograph is an interactive program that computes numerically,
then graphs solutions to systems of ordinary differential
equations (ODE's) and difference equations. The program is
capable of solving systems of n simultaneous DE's or difference
equations. Biograph is a menu driven program, but the menus are
a little hard to understand. For example, when you are in a menu
other than the main menu you have no way of knowing that the
command F10 will return you back to the main menu. Also, the
graphics are not very sophisticated. For example, the axes are
not marked by the variable they represent. There is also great
difficulty in creating your own file, I wasted a lot of time
trying to create my own model and was unable to do so. (This
program is not at all user friendly!) However, other than that I
think that the program is good. It has a lot of options such as
saving data to a file, retrieving data previously saved, output
data, changing parameters in already existing models, changing
initial conditions, or determining the limits of the axes for a
graph. You can also determine equilibrium points, get a phase
plane, and graph every variable versus time axis. (REVIEW
1:RATING=7)
This software was very hard to use. To begin with, the
descriptions on the main menu are not very explanatory. I had a
hard time relating what I wanted to do with the choices
represented on the menu. I even looked at the user manual, but
it was very little help to me. For example, when you are in one
of the submenus and press 'q' to quit, it does not return you to
the main menu, instead it returns you to a black screen with no
indication where the cursor is. This was confusing to me, and I
had to randomly press keys until I found out that you press enter
in order to make the main menu appear. When I retrieved a
document and had the program graph it for me, I did like the all
the information available about the graph, but I thought the
graph itself looked plain compared to software I have already
used. In my opinion, this software would be frustrating for a
naive user to work with. When compared to Models or Phaser, this
software is easily the most difficult to execute and work with.
The program itself would be good to solve differential and
difference equations because it provides the user with great
options in order to examine the graphs and solutions of the
problems. However, it requires a great deal of time in order to
be able to execute the program successfully. (REVIEW 2: RATING =
6)
For review refer to THE QUARTERLY REVIEW OF BIOLOGY December 1990
volume 65 page 539.>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Bergdoll, S. and J. Grethe (1991) BioSimPC, ver 2.0 (BASF-AG)
[PC, WINDOWS, SIMULATOR, NEUTRONS, BIOLOGY]
<This is a simulation program for neurons. The program allows
the user to input information about the types of neurons and
synapses to be simulated. The user must know a lot about the
biology of neurons to use this program. The graphics are very
nice. There is help available, but again, one must know the
biology. This package would be good for someone who knows about
nerves and wanted to explore different nerve connections. There
are some sample files, but a more structured example would have
been very helpful. Overall, the program is well done and could
be very useful for certain fields. (Review 3: Rating 6)>
From: LISTING OF SOFTWARE QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Goburn,Alex (1990): BIOSIMS. (130 Browood # 621, FT Collins, Co
80521, phone (303) 221-9489) [BIOLOGY, ECOLOGY, GENETICS,
POPULATION <The programs in BIOSIMS are very simple - each is
good only as an introduction to the subject. For example the
Population Growth model contains only three models, exponential,
logistic and growth with lags. You have the option of changing
the parameters such growth rate initial population, carrying
capacity and # of generations you want to simulate. You have no
way of printing out the graphs other than print screen and there
is no on-line help. In fact, I have written a program doing the
same exact thing using MATLAB. It took about an hour to do that
so I don't think it is very exciting. The second program Action
Potential is also very simple. The process is this: you enter an
initial membrane potential then change the membrane potential
with a stimulus. You then observe the action potential and the
associated Na+ K+ conductance change. Again, there is no help
(which is probably not needed because of simplicity of program)
and no way of printing. The third program Gene Plot is good only
for a classic population as the author said, "in the classic
population there are only two alleles which may produce a total
of three different genotypes. In this model phenotype is
implicit and selection only works on genotypes. Although in
reality you can only select on phenotype this is a good model to
understand the concept of " natural selection." Again there was
no way of printing. In this program there was a help option, but
the problem is that if you chose this option you can't quit in
the middle of the help menu you have to scroll through the whole
thing to get out. Overall these programs are good only as
introduction to these subjects though they are user friendly.
(REVIEW ?: RATING = 6)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Dawkins,Richard (1987): Blind Watchmaker. (W.W. Norton, New
York) [BIOLOGY, GENETICS, MAC<This is a really nice package.
It allows the user to set the mutation rate for a species. There
are a number of different species that one could use. All of the
species are merely graphics. The mutation of the species is a
process of different symmetries. The package is well written and
very friendly. It is a nice graphics display that allows the
user to see the effect of mutation. This program is a simple one
that would be useful in a genetics class for seeing mutation
effects. (REVIEW 3: RATING 9)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Kreitzer,GP; Borisyuk,RM (1989): Catching Fish. (Applied
Biomathematics) [ECOLOGY, SINGLE POPULATION, DOS<This is a game
of catching fish. Each game consist of ten seasons of fishing,
and you can adjust the intensity of fishing at the start of each
season. One set consist of five games, but you can extend it to
ten games. You can view previous games within a set by selecting
the "View Game" function. You also have the option of saving any
interesting game on a disk. You can restore them, as well as the
relevant parameters, and continue the game with these parameters.
For saving, loading and deleting, select the "File" function.
However, you can only save this information for one session- you
lose all information if you quit the session. If you over-
fished and caused the abundance to fall below the critical value,
the prompt "Poor fish!" is displayed and the score will be
negative (i.e. you doomed the population to die out). A simple
easy game to understand but in my opinion it fits more students
that are in high school. (REVIEW 1: RATING = 7)
This program teaches the user the impact of fishing on the fish
population by making it a game the user can play. The software
was really user friendly and commands were easily accessible.
The user can simply move to the command s/he wants with the arrow
keys and indicate this command by hitting enter. I liked the way
that the graph appeared as you were playing. The only problem I
had with the game is that there is no way to save information
from one use to another. In my opinion, this software could be
used by anyone, and could prove informative if someone wanted to
learn the effects of fishing on a fish population. (REVIEW 2:
RATING = 7)>
From: LISTING OF SOFTWARE (7/93) QUANTITATIVE CURRICULUM FOR LIFE
SCIENCE STUDENTS (Supported by NSF Grant)
REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff
For more information contact: Dr. Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]
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Curacao. PC, GENETICS, BIOLOGY, WINDOWS
This is a nice program that allows the user to manipulate a model
of the sterile insect release method. The program is easy to use.
There is on-line help available that is very useful. The program
offers good graphic and verbal conclusions. The problem is set up
with the user setting the parameters. Then the solution is run one
generation at a time. The program is useful for the model it is
designed for. (REVIEW 3: RATING 7)
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Marck,Christian (1990): DNA Strider 1.0. (Institut de Recherche
Fondamentale, France) [BIOLOGY, GENETICS, MAC <This program
allows the user to convert potential DNA sequences into their
respective proteins. The program is not friendly at all. I had
a hard time figuring out what was going on. There seems to be no
instructions included. The program requires a DNA sequence to be
put in. This is a long and tedious process. I did not see much
that was very useful in this program. (REVIEW 3: RATING 2)>
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Lapin,Lawrence (1987): Easystat. (Harcourt Brace Jovanovich
Inc.) [STATISTICS, DOS<This is an easy software to understand
and to get familiar with. The main menu looks like this: "Main
Menu: File Edit Column Stat Utility Help Quit." Each of the above
options requires no background to understand except the Stat
option. Its menu looks like the following: Stat Menu: Summary
Hist Probability Regression ANOVA Chi Std.Err Time Non-para. In
order to use this menu you need to understand the above basic
statistical terms. This program has a lot of nice options such
as being able to fill a table randomly giving the upper and lower
limits. You are able to edit a table, print out a table, graph a
column versus another, copy one column to another, or delete a
column. You also have a help screen. You are able to perform
arithmetic operations on any column (add, multiply, divide,
power, logarithm, etc.) In general, this is a nice and easy that
need only elementary background in statistics. However, the
graphics are not very sophisticated, and they can sometimes be
confusing because they graph only coordinates and do not connect
them. Also, it doesn't give error messages when you enter the
wrong input instead it freezes for some time and then comes back.
(REVIEW 1: RATING = 7.5)
This program is similar to a spread sheet with many statistical
applications. For this reason, I think that most people would
find it easy to use, especially if they have worked with spread
sheets before. The menus are nice in the fact that when you
highlight a menu it prints underneath what options are included
in that menu. This makes it easy to access whatever operation
you want to perform. I liked the various options the program had
concerning the manipulation of data. For example, I liked the
fact that you can randomly fill a column with data you have
already entered. I liked the fact that the program graphs
information for you, especially one column against another, but
the graphs are not very sophisticated. I thought the statistical
options were very nice. I feel this software would be useful to
students who wanted to apply statistics to real situations. I
think that it could be used with a class in order to help
students apply the distributions they usually only read about.
It would also let them compare various distributions. In my
opinion, this software is simple to use and could very easily be
used by students taking statistics. The only problem I had with
the program is that there are no error messages, and on some
occasions I found myself having accidentally escaped the program
before I realized what was going on. (REVIEW 2: RATING =8)>
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Exeter Software (1990): Ecological Computer Games. (100 North
Country Rd. Setauket, NY) [COMPETITION, ECOLOGY, MULTIPLE
POPULATIONS, PREDATOR PREY, SINGLE POPULATION, DOS<The games
can be a good lesson for students. They can explain how one can
choose a strategy in order for the species in a predator-prey
system to survive. (For example, the fox and rabbit game.) In
the Hawk, Weasel and Mice game the speed of the opponent was
always faster which made it difficult for me to win or make the
three species survive. It was frustrating. The same with the
Rabbit and Fox game. However, I liked the Trout game the most.
I was able to crash the species or make the species grow
logistically. It seemed to me that the best strategy for this
game is to stay on the surface and eat only insects. A nice
thing about the three games are the graphs that show the change
of each species with time. (REVIEW 1: RATING = 7)
This software teaches you about populations while also allowing
you to participate in a game. I think the fact that the user can
play a game makes it more appealing to use. The Trout game was
fun, but the other ones made it very difficult to win, because
the prey and the opponents move a lot faster than the predator
that is being manipulated by the user. The program was really
user friendly and easy to use. It also offered good explanations
for what was happening and graphs. The only things I did not
like about the program was that once you start the program you
cannot quit without playing a round nor can you change the speed
of the participants without quitting the program and starting it
over. In general, I think that the program can teach a student
about how populations crash or thrive based on energy and food
consumption while making it into a game. (REVIEW 2: RATING = 7)>
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Chariot Software Group (1988): Ecology Stack, Geology Stack,
Science Stack. (CSG Pub Domain/ SW Library) [ECOLOGY, GEOLOGY,
MAC<Ecology Stack: This software is nothing but a tutorial disk
that presents ecological questions and topics on related talks,
maps, etc. Geology Stack: Again this is a geological tutorial on
projections of maps etc. Science Stack: It contains a demo of
Macrograde a software that is used by instructors to keep records
of students' grades etc. It also contains nice Astronomy slides
and a demo of the software Physics test. It is only a tutorial.
(REVIEW 1: RATING = 2)>
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Host,E; Rauscher,M; Iserbrands,J; Dickmann,D; Dickson,R; Crow,T;
Michael,D (1990): Ecophys. (U.S Dept. of Agriculture, 1992
Folwell Ave., St. Paul, Minnesota 55108> [BIOLOGY, ECOLOGY,
PHYSIOLOGY, DOS<This is an explanatory whole-tree process model
that simulates the growth of Populus during the establishment
year. Ecophys allows the user to change physiological based
factors that influence the growth of Populus. It is helpful to
know how these factors affect growth in order to identify a
genetic selection criteria, which may be used for the selection
and breeding of poplar clones. The program consists of three
primary modules which control the actual simulation and several
supporting modules which allow physiological, environmental, and
simulation parameters to be modified. In a typical run the user
chooses form the main menu the desired clonal and environmental
conditions, specifies the beginning and ending date for the
simulation, and selects the screen and printer reports to be
generated during run. Once all initial conditions are specified,
the user selects RUN SIMULATION from the MAIN MENU and the
program control passed to the SIMULATE module. SIMULATE keeps
track of the hours and days and passes control to HOURSTEP or
GROW modules, as appropriate. When the ending date is reached
summary of reports are printed or written to disk files, and
program control is passed back to MAIN MENU. At this point a
graphic representation of the tree may be viewed on the screen or
sent to a plotter for output, in my opinion the graphics are not
very clear nor very sophisticated. Other than this I thought
that this is a very good model. It can be used to simulate the
growth of poplars under varying environmental conditions,
simulations that would be difficult to conduct as field
experiments, and it is easy to use and get familiar with in a
short time. (REVIEW ?: RATING = 7)>
Price,Frank E; Vaugham,Virginia (1989): Evolve. (BioQUEST)
[GENETICS, MAC<This is a program that allows you to experiment
with evolution and to get quick results that are impossible to do
any other way. You may control the starting population, overall
population size, natural selection, pattern of inheritance, and
migration in a hypothetical population. It provides you with a
practice of posing evolution questions and trying to use various
strategies to answer these question. It also provide data and
graphs that help answer the questions. Evolve is very user
friendly and in my opinion a first year college student can gain
an understanding of evolution and natural selection ideas.>
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Statgraphics (1991): Execustat. (PWS-KENT Publishing Company,
Boston) [STATISTICS, DOS<This is the most wonderful statistical
software, I have played with so far. You can almost do
everything without using the manual. It has wonderful three
dimensional and two dimensional graphics. It has all the options
you can imagine on the axis such as rotating, resizing, etc. It
is easy to make your own file, save files, print files, load
files, etc. Every time you enter a command, it provides the user
with options for input. This option makes it where the user
cannot enter incorrect data. It is a good software that could be
used by students or professionals. Basically, I did not find
anything wrong with this software, and I would recommend it for
anybody. (REVIEW 1: RATING = 9)
I really enjoyed using this software. Its capabilities seemed
unlimited. The program is very user friendly, and I was able to
enter my own data, make three dimensional plots, rotate the
plots, and analyze the data without having to use the help
command or consult the user manual. The commands are always
listed in front of the user, and the user must merely select what
he wants to do and press enter. I was really impressed by the
fact that when the computer as you to input data, it gives you
choices. For example, it will prompt you to enter a variable and
underneath it list the possible variable names that you might
select. I also liked the fact that when you retrieve files it
list the files available to be retrieved. This saves the user
from having to remember what he named files or from having to
exit the program and look in the directory for data files. The
graphing capabilities were great. The program has all kinds of
graphs from simple histograms to three dimensional plots where
the user can rotate the axis. Another thing I liked about the
program is that when you select different ways to analyze data
there is always an interpret option. This option explains
exactly what the data is telling you and what everything means.
I think that students taking statistics or probability would
really find this software useful. The program would certainly
help students visualize and analyze data while at the same time
being user friendly. (REVIEW 2: RATING = 9)>
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Lo Cascio,NJT (1990): Forecasting Gene Frequency. (Wisc-Ware)
[BIOLOGY, GENETICS, DOS <This is a very simple program in my
opinion that could be written by a freshman or sophomore student.
It has a main menu that gets to three other routines: one to make
a Chi-Square statistical test, second for genetic projections in
Sickle-Cell Anemia, and the third for genetic projections in
hemophilia. If you don't want the output to go to the printer
you must turn the printer off because the output automatically
goes to the printer and you have no choice. There is no help
menu or command and a lot of other missing options. Overall this
is not a good software. (REVIEW 1: RATING = 2)
This software is really simple. To me, it merely offers
explanations about chi-square, sickle cell anemia and hemophilia.
Most of the program consisted of written paragraphs about these
subjects. One problem I had with it was the fact that it
automatically prints everything when ever you press an option.
This is really unnerving. There are very few options concerning
saving data or manipulating data or error messages. For example,
if you incorrectly enter a value you get an error message that is
dealing with the program, and you don't receive a message to
re-enter a value or that the value is not within a correct range.
The program is too simple to be of much use, but it could be used
by practically anyone. In my opinion, the program would have
very little to offer a user except for information about sickle
cell anemia or hemophilia. (REVIEW 2: RATING = 2) For review
refer to THE QUARTERLY REVIEW OF BIOLOGY June 1991 volume 66 page
242>
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Calley,John; Collins,Angelo; Jungck,John (1990): Genetics
Construction Kit; A project BioQUEST simulation. (BioQUEST,
Biology Dept., Beloit College, Beloit, WI 53511) [BIOLOGY,
GENETICS, MAC<This program is very good at allowing the user to
cross organisms in order to determine the inheritance patterns of
a particular trait. The program did a good job of allowing the
user to decide how to cross organisms. For example, the user can
decide whether to cross two organisms which have the same genetic
make up or cross two random organisms. Also, the program keeps
track of which crosses have been made and in which vial these are
stored. This aspect of the program is real handy, because it
helps the user keep track of what he has done while at the same
time helping him locate previous crosses. Another aspect of the
program that made it easy to use was the fact that the program
counts for the user, and the user is able to decide if he wants
to see the total number of organisms with a certain trait or if
he wants to see the number of each sex with a certain trait. I
also found the data to be realistic, because on some simulations
it took a couple of crosses before any conclusion could be made
about the organisms inheritance. This is very similar to what
could occur in a real lab. There was only one thing I thought
the program should have included. That is I think it should
display ratios. Since the program counts and classifies each
generation, I think it should also demonstrate a ratio. It
certainly would help the student decide what alleles are present.
However, in general I think the program is a good simulation of a
real lab where students start with organisms they know very
little about and try to draw conclusions about their inheritance
by crossing them. In fact this may be better than doing the real
lab, because it allows the student to cross organisms and get
results in a fraction of the time. (REVIEW 2: RATING= 8) (REVIEW
1: RATING = 8)>
(1990): Isolated Heart Lab. (BIOQUEST, Biology Dept., Beloit
College, 700 College street, Beloit, WI 53511) [BIOLOGY, MAC]
<This program is designed to allows the user to conduct his own
experiment in order to answer the question, "Does cardiac output
change with heart rate? inotropic state? peripheral resistance?
or preload?" Within the lab itself the user is able to choose
which of these four things he wants to experiment with. The
choices include: diastolic function, systolic function, afterload
effects, effects on heart rate, or tutorial problem. When a
choice is made the user can edit the input in any manner he wants
in order to see how this will affect cardiac output. The program
is user friendly in the fact that it highlights the input that
the user is able to change. Once the information has been edited
you can begin the experiment. The user can select start, and
then the program will graph information as the data changes over
time. The user can stop the program, or it will stop
automatically after a given time. The program gives the user the
option of what s/he wants plotted. The choices include: left
ventricle pressure and volume versus time, left ventricle
pressure versus volume, or left ventricle pressure and arteriole
pressure versus time. The program also allows the user to
perform several trials. The program in general is user friendly
because commands are easily understood and performed using the
mouse. However, I was not able to figure out how to print out
information or if that option is even available. Besides the lab
itself, the program has an Isolated Heart Lab Introduction. I
thought this was very nice. This part of the program includes:
an introduction (which gives definitions and the purpose of the
software), the heart plumber's kit (which allows the user to
perform a bypass in which the user selects whether he wants to
use a valve, ventricle or vessel in each of four spots), pressure
time animation (which shows an EKG at the same time it shows the
heart pumping with a description of each movement and the user
can hold the mouse down to see continuous pumping or go frame by
frame to understand each section), and a pressure volume loop
animation (which does the same thing as pressure time animation,
but also includes a volume graph). This part of the program was
the most impressive because the frame by frame descriptions of
the heart pumping allows the user to visualize what exactly is
happening while reading about it. In my opinion, this software
would really be useful to someone who is studying this subject
matter. I was able to learn a lot of things just by running the
animations, and I feel that someone who is studying this material
could learn even more. Overall, it is a friendly software
especially if you understand the subject matter. (REVIEW 2:
RATING = 9)> <The heart lab is an excellent simulation of heart
function. The simulation enables one to explore how the
ventricles of the human heart performs as a blood pump and to
characterize changes that alter its performance. The program is
so simple to use that even those with very little knowledge of
the physiological function of the heart may find it educational.
The program does on graphs what a textbook does in several
chapters. The simulation is very widespread in its variations;
it seems to answer almost any question one may have concerning
the function of the heart. Although heart lab is informative,
the graphs are dull. The program could be more exciting if the
diagrams were more life-like. Watching the same graphs tend to
become boring after a period of time. A life-like heart with
actual movement would have made this program superb. If it were
just cartoon-like, it would be even simpler to use and more
exciting to watch. Using the program is probably the closest one
can get to hands on experience in the area of cardiology other
than working with patients. The program still provides one
simple advantage over working with patients and that is the
ability to experiment with different variables and get immediate
results. Such a program as Heart Lab might be used as a
reference to physicians or medical students when examining heart
variations.>
-----------------------------------------------------------------
[MACINTOSH, STATISTICS, REGRESSION].<This is a statistics
package. It is very useful for basic level statistical analysis.
The program comes with a spread sheet with allows the user to
input data without exiting to program. The program makes very
nice plots. The package will also do regression and some of the
simpler tests, e.g., the t-test. There are many examples
included with this program. The manual is also easily read and
understood. The biggest problem is that the information does not
fit on the screen. It is slightly annoying to have to
continually more the screen around to see what doesn't fit.
Overall, this is a very good introductory statistics package.
(Review 3: Rating 7)>
Levitan,Herbert (1988): LOGISTIC. (Wisc-Ware) [BIOLOGY, ECOLOGY,
SINGLE POPULATION, DOS-WINDOWS <This program is based on the
simple logistic differential equation. It is a very easy program
to use with Windows (which has nice graphics) and a mouse. It
gives you the option to change I.C. and other parameter values
in the equation. There is no print out option, but there is
nothing much to print since all you have is one window which is
half data and the other half is for plotting the data. However,
the software serves the objectives of the author. One of these
objectives is to encourage students to use computer simulations
as a tool for learning. I think that this objective is met
because of the simplicity of using this program. Hopefully
students will be encouraged to use other simulation programs that
may be more involved after using this one. The program has an
example of the discrete logistic chaos graph that students may be
interested in seeing, and also students can input data that makes
a population go extinct. Overall, this is not a very complicated
program; however, the author does mention that it is based on
simple logistic equation. (REVIEW 1: RATING = 6)
The logistic software is very simple to use. The fact that it is
used with Windows makes options easily accessible, and also makes
everything easy to see. The program itself is real simple and is
easily understood. I liked the fact that it is very easy to
change data, and if you plot one set of data you can leave it on
the screen and compare it with the next group of data you enter
and plot. However, in general the software seemed very simple
and limited in its applications. In my opinion, the program
would be easy for anyone to use, but would be of little use to
someone because it is limited in what it does. (REVIEW 2: RATING
= 4)>
-----------------------------------------------------------------
Maddison,Wayne P; Maddison,David R (1993): MacClade. (Sinauer
Associates, Inc. Publishers, North Main Street, Sunderland, MA
01375) [ECOLOGY, MAC, MODELING <MacClade is a program that
provides theory and tools for the graphic and interactive
analysis of phylogeny and character evolution. The program
reconstructs and displays character evolution on the phylogenetic
tree, and, as the user manipulates the tree on screen, MacClade
gives feedback via tree graphics, statistics, and charts. Latest
version is 3. This package contains some very interesting AIDS
information as the sample data. The package is somewhat
confusing for how to use it. (REVIEW 3: RATING 4)>
John H. Hubbard; West,Beverly H (1992): MacMath. (MacMath,
Springer-Verlag) [CALCULUS, COMPETITION, DIFFERENCE EQUATIONS,
DIFFERENTIAL EQUATIONS, ECOLOGY, LINEAR ALGEBRA, MODELING,
MULTIPLE POPULATIONS, PHASEPLANE, POPULATION, PREDATOR PREY,
SINGLE POPULATION, MAC<The software was designed to supplement
a junior or senior level class in differential equations. I, as
a junior, found the software easy to work with and easy to
understand. It is very useful as a tool to graph differential
equations in two or three dimensional space. When I used the
software with the manual, I was able to create really neat
examples. What I liked about the program is that it is very
versatile. The fact that it combines several programs in one
would make it a useful tool that could be used for various
classes as an undergraduate. In my opinion, this software would
definitely be very helpful and easy to use for an undergraduate.
(REVIEW 2: RATING = 8)
This software can only be used for class demos and for
undergraduates in general. It has several separate programs
which include an analyzer which graphs a general function and
finds its roots, differential equations which have two and three
dimensional aspects with phase planes, a demo for bifurcation, an
eigenvalue and eigenvector solver program, a numerical methods
program for solving differential equations (Runge Kutta, Euler,
Midpoint Euler), Fourier approximation for any given function,
and others which are not important for our discussion. Because
this is a Mac program, it is very simple to use, everything
except input of data can be done with the mouse. The thing I
liked the best was its eigenfinder program. This program gives
the output in a very nice mathematical manner; however, it is
limited to twelve by twelve matrices. In the phase plane
program, you can start the trajectory any place you want on the
screen by pointing the cursor and clicking the mouse. This
aspect is a time saving device because the user doesn't have to
plug in initial conditions. The three dimensional graphics were
not very good. However, it serves the purpose in which it was
intended. (REVIEW 1: RATING = 8)>
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Myers,Gene; Blanco,Carlos; Jahnke,Jerome; Hallick,Richard (1990):
MacMolecule. (University of Arizona) [CHEMISTRY, MAC<This
program takes organic molecules and provides the user with a 3-D
model of the structure. The program has a complete list of
molecules that are very common in chemistry. All the user must
do is select the molecule, and the program provides a three
dimensional representation of the molecule. Once you are viewing
the model, there are other options that can be selected. The
program will allow you to rotate the model in any direction you
want by simply taking the mouse and clicking it in the desired
direction, the computer will continuously rotate the molecule in
any direction you choose until you indicate to stop, or you can
indicate in which direction you want light rotated. This program
is really user friendly in the fact that all the user must do is
click the mouse on the model s/he wants to use and then select
the options s/he wants to perform (all of which are easily
understood). There were only two problems I had with the
program. One is the fact that the model represents different
elements within the compound with different colors without
indicating what color goes with what element. Also, I think the
program should include an empirical formula for the compounds
being graphed. Besides these problems the program does a great
job of demonstrating compound in three dimensions. I feel this
program would be of great use to students who are trying envision
compounds in their minds. The software is certainly a lot easier
to use than the model building kits currently being used in
chemistry classes. In my opinion, this program would be of great
use to someone studying chemistry or learning about organic
molecules in biology (e.g. DNA). (REVIEW 2: Rating= 8)
This software is designed for teaching molecular structure to
students of biology, chemistry and allied fields. It begins with
discussion of small biological molecules such as amino acids,
lipids, nucleotides, sugars, and vitamins. Then, this is
followed by larger molecules such as DNA and RNA. Students can
use data from molecular structure data bases and create 3-D
models of small and large molecules on computer screen. Users
are able to interactively rotate the image in the x, y, z axis on
the computer screen. The images can be saved to a disk as a
sequence of PICS images that can be replayed from MacMolecule as
an animation sequence. Very nice images and rotation, user
friendly software. (REVIEW 1: RATING = 8)
Very nice graphics. Well-written program. (Review 3: RATING = 8)>
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Chariot Software Group (1988): Math 1. (CSG Pub Domain/ SW
library) [ALGEBRA, MAC<I played with this software for over an
hour. It has a lot of options when they work. The things that
work correctly are the 2-D graphs, the fractal, the Mac Lin 1.0,
and the tangent options. I managed to crash the 3-D graphs
several times on different easy functions like z= x**2 + y**2 for
example. I managed to crash the conformal maps option, and I was
unaware of what I did to make the program crash. In other words,
the program is in need of a lot of fixing and modifications.
(REVIEW 1: RATING=2)>
-----------------------------------------------------------------
Chariot Software Group (1988): Math 2. (CSG Pub Domain/ SW
library) [ALGEBRA, MAC<This is a simple program. The option
MathMaster is designed to solve first year algebra problems. It
has an equation editor to create integral summations, fractions
square roots and matrices. It has a number investigator that
gives information on integers up to twelve digits such as prime
factors, hexadecimal equivalents, and binary equivalents.
Scientist's helper is data analysis / graphing program. Simple
graphing, data reduction, multiple regressions, filtering,
Fourier transform, etc. are also available. (REVIEW 1: RATING =
2)>
-----------------------------------------------------------------
McDonnell,Eon (1990): mDNA. (intellimation, P.O. Box 1922,
Santa Barbara, CA 93116-1922.) [BIOLOGY, GENETICS, MAC<This
program provides a student with a tool for exploring different
mitochondrial DNA models. The student gives the initial values
s/he wants such as population size, number of generations, length
of an individual (up to 400 sites), and the restriction enzyme
used. In the simulations, family trees are continuously updated
to show current inheritance structure. The student is able to
pause the simulation at any time to show DNA, highlight similar
groups, or inspect mutations. One can save pictures or data to a
file for later use, but this file cannot be printed out using
MacPaint or similar software. Over all, this is a good program
and has a good help facility to help get you going. (REVIEW 1:
RATING = 6 ) (REVIEW 3: RATING = 5)>
-----------------------------------------------------------------
Calley,John; Jungck,John (1990): Microbial Genetics Construction
Kit (BIOQUEST Software). (BioQUEST, Biology Dept., Beloit
College, Beloit, WI 53511) [BIOLOGY, GENETICS, MAC<This program
was designed to allow students to perform experiments with
bacteria to simulate experiments that might be performed in a
real lab. The software begins by giving the user a main menu.
Here the user can choose one of five options: Serial Dilution
Tour (which is designed to allow the student determine the number
of bacteria in a random sample), Phenotype Identification Tour
(which allows the user to determine the phenotype of the bacteria
based on replication), Complementation Tour (which allows the
user to perform experiments to decide if two organisms that need
the same nutrient to grow can benefit each other), Conjugation
Tour (which allows the user to conjugate a colony) and Full Menu
(which includes all of the options above). This menu is in
increasing order of difficulty. For example, if you start off
experimenting with the Serial Dilution Tour and master this
section, then you select the next option (Phenotype
Identification Tour) it builds on the first option. This would
be very helpful to a first time user who could gradually work
his/her way through the experiments and by the time s/he chooses
the Full Menu option, s/he would be familiar with everything the
program has to offer. In the Serial Dilution Tour, the program
provides the user with a test-tube of unknown bacteria. The user
must dilute the test-tube until s/he is able to count the number
of colonies that are present. I liked the fact that the computer
keeps track of the power to which you have diluted the bacteria
and the fact that if you select the test-tube history option, the
computer will tell you information about that particular
test-tube. In Phenotype Identification Tour the computer gives
you a petri dish with colonies. The user can then replicate the
plate and choose which nutrient or antibiotic s/he wants present
on the new media. In this section, the Media Matrix and the
Phenotype Worksheet make it easy to view what experiments you
have performed. The matrix indicates what nutrient or antibiotic
is available on which petri dish and the worksheet allows the
user to input his/her own data (s/he indicates whether or not
s/he has found each nutrient necessary or not and whether the
bacteria is sensitive to each antibiotic.) To me, these two
options make it very easy to keep track of experiments and
conclusions. In the Complementation Tour the same options are
available as before but now the user is also provided with
complementation worksheet for which the user indicates which
nutrient s/he is working with. Also, there are several options
that let the user decide if he wants to inoculate a tube with a
colony on the same media or different media or plate a tube on
the same media or different media. In the Conjugation Tour, all
other options are available, but now the user can conjugate two
colonies. In general, I found the experiment realistic, because
it took several experiments before any conclusions could be made-
just like in a real lab. Also, the computer leaves it up to the
user to make conclusions- just like in a real lab. In my
opinion, this software would be simple for someone who had a
knowledge of a MacIntosh and would also help educate the user on
the subject matter. (REVIEW 2: RATING = 8)>
-----------------------------------------------------------------
Salmon,I (1986): MicroModeller. (IRL Press (Oxford University
Press), Oxford) [ECOLOGY, POPULATION, DOS<For review refer to
THE QUARTERLY REVIEW OF BIOLOGY March 1990 volume 65 page 131>
-----------------------------------------------------------------
Lapidus,Martin (1990): Models. (Lascaux Graphics 7601 N. Calle
Sin Envidia #31 Tuscon, AZ 85718) [CALCULUS, DIFFERENCE
EQUATIONS, DIFFERENTIAL EQUATIONS, ECOLOGY, MODELING, MULTIPLE
POPULATIONS, POPULATION, SINGLE POPULATION, DOS, MAC<A very
nice software for solving difference and differential equations.
I found it to be very fast. In fact, I have tried a difference
equation that was implemented first on Mathematica (not in the
most efficient way), and Models was much faster and easy to
implement. We got to see the two and three dimensional graphics
easily and nicely, and we had the option to zoom in and out on
any part of the graph. I liked the ability of being able to
rotate the axes and the fact that it is able to solve a large
system of equations unlike Populus which could handle a maximum
of four equations. This software also allows you to set the step
size for integrating the ODE, which is something that comes in
handy when you know some information about the ODE you are
modeling. One disadvantage is that if you have a large system of
ODEs that can be defined iteratively using a DO LOOP then it
would be tedious to use models because you must enter each
equation separately. In my opinion, this was one of the best
software programs I played with (for DE's). I highly recommend
this for junior or senior level students, graduate students, and
professionals. (REVIEW 1: RATING = 9)
The program is a very good tool to help students visualize
difference and differential equations. The software overall was
simple to use and would require very little knowledge of
computers. The only problem I had with the package is that it
was difficult to use without a mouse. When used on a computer in
which I could use the keyboard only, I found it difficult to
figure out how to do different things. However, when the mouse
was available, the program was easy to use, and I enjoyed using
it. In my opinion, Models is a very easy to use software which
would certainly be useful to students in at any level who are
dealing with difference and differential equations. (REVIEW 2:
RATING = 9)>
-----------------------------------------------------------------
Press,William H; Flannery,Brian P; Teukolsky,Saul A;
Vetterling,William T (1988): Numerical Recipes. (Cambridge
University Pres, Cambridge and New York) [NUMERICAL ANALYSIS]
<For review refer to THE QUARTERLY REVIEW OF BIOLOGY March 1989
volume 64 page 115.>
-----------------------------------------------------------------
McKelvey,Kevin; Crocker,Jennifer (1992): OWL. [BIOLOGY,
GENETICS, DOS, MODELING <A spatially explicit system for
modeling demographics and genetics of the spotted owl. This
modeling system consists of five individual program which allows
you to create a map of a specific land configuration, to place
owls, to modify the rules that govern model behavior, and to
produce condensed output.>
Curtis,Dave (1990): PEDRAW. (Academic Department of Psychiatry,
St Mary's Hospital Medical School Praed Street, London W2 1NY,
England, e-mail [log in to unmask]) [BIOLOGY, GENETICS, DOS]
<PEDRAW is a program which draws out family trees in either text
or graphics mode. It is designed to be used to help with
genetics research, especially linkage analysis using the LINKSGE
and LINKSYS packages. Data about the structure of the pedigree
and about the individuals within it is read in from a data file
which can have one of a variety of formats. One individual is
selected and his/her relatives are displayed either
diagrammatically using shaded symbols or else as paragraphs of
text linked by the IBM box character set. The pedigree is saved
to disk in either Microsoft Paint Format or as a text file.>
Will,Ed (1987): Plant Kingdom. (HyperCard) [BIOLOGY, MAC,
TAXONOMY<This program is very similar to the Animal Kingdom
program. It has the same problems. It has more than just the
Plant kingdom. There are also fungi and some algae. The basic
problems remain that the program is not very user friendly and
that there seems to be a very limited application for the use of
this program. (REVIEW 3: RATING = 4)>
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Wilkinson,HT; Pederson,WL; Pondy,K (1989): Plant Root Model.
(Wisc-Ware) [BIOLOGY, ECOLOGY, PHYSIOLOGY, DOS <A very simple
program that has only two screens- one for changing data and the
other is a screen for the graph of the volume of the rhizosphere
where you can see it in three different directions (upper, side,
skew). In the data screen you can change the biology and the
edaphic factors in the soil which in turn changes the max
distance that the fungus can grow to the root and infect.
(REVIEW 1: RATING = 1)
This program is very simple and is very specific. In order to
use this software, the user would have to want to observe a
rhizosphere otherwise the program would be useless. I did not
like the fact that it simply showed you a sphere around a root
with no reference to distance or why it gets smaller if you
change certain factors and larger if you change others. Even if
the user changes the influence, there are very limited
possibilities, thus making the software useless after all
combinations of influences have been observed. The only thing I
liked about the program was that it had a good explanation about
what rhizospheres were, and it was simple to use with windows.
In my opinion,the software would not be beneficial to students.
(REVIEW 2: RATING = 1)>
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Etter,Ron; Maddison,David (1992): PopDyn. (EcoSoft, Inc., 7
Noble Hill, Beverly, MA 01915). [BIOLOGY, ECOLOGY, MULTIPLE
POPULATIONS, POPULATION, SINGLE POPULATION, MAC<This program
seemed to be designed to demonstrate the graphs of population
dynamics. The program does not allow the user to use their own
equations, it simply allows the user to adjust constants. To me,
this type of program is not very useful, unless a student wanted
to see the graph of general logistic, exponential, predator-prey
or competition equations and even then once you've seen the
equation there is nothing really else to see. The graphs were
cute, and it was really easy to change the parameters so it is a
very user friendly program. Other options in the program include
looking at different models in three dimensions. This part of
the program again showed really colorful and pretty graphs, but
the graphs lacked explanation. It was really easy to rotate the
axis of the graphs, but you cannot rotate the graph itself when
you rotate the axis. Instead, the current graph is automatically
erased and the user must redraw it. To me, it was difficult to
visualize the graph because it did not rotate when the axis did.
Also, the program has a group of files that you can look at.
These include great pictures that people obviously have created,
but again there is no explanation or equations that the user can
relate these graphs. Instead, they just seem to be nice
pictures. In my opinion, this program has very little to offer
students, unless they just want to see demonstrations of general
population dynamics equations. (REVIEW 2: RATING =4)
This software is designed for demonstration purposes in class.
One of the things I enjoyed very much is that in the competition
model, the user is able to move the isoclines anyway he wants
which allows him to change the parameters and thus changing
equilibrium and then it allows you to see the phaseplane of the
two species. However, it is limited in the sense that it has
only four models exponential, logistic, Lotka-Volterra
predator-prey and competition models. One thing I did not like
about the program is that it does not allow you to edit or enter
equations. It has a nice chaos demo of predation and competition
three dimensional model. The graphics are nice. It is very good
software for somebody who has a course in differential equations
(sophomore or junior level). (REVIEW 1: RATING = 7)>
This program is nicely done and easy to use. The read me file
gives a good description of the package. (REVIEW 3: RATING = 7)>
-----------------------------------------------------------------
Berryman,Alan A; Millstein,Jeffrey A (1988): Population Analysis
System (POPSYS). (Ecological Systems Analysis, Pullman,
Washington) [ECOLOGY, MODELING, SINGLE POPULATION, DOS<For
review refer to THE QUARTERLY REVIEW OF BIOLOGY March 1990 volume
65 page 130>
-----------------------------------------------------------------
Towner, H.: Population Ecology And Genetics. [ECOLOGY, GENETICS,
POPULATION, APPLE DOS<For review refer to THE QUARTERLY REVIEW
OF BIOLOGY September 1992 volume 67 page 425>
-----------------------------------------------------------------
POPULUS. The Populus software contains a set of simulation
models that we use in teaching population biology and
evolutionary ecology at the University of Minnesota. All of the
simulations share a common format, as follows: After a model is
chosen from the menu, the program displays (optionally) several
screens of background material which introduce the mathematics
and end with basic references. Next, there is a screen listing
all of the input parameters; students can move among the
parameter boxes and change initial defaults to values of their
own choosing. The program maintains a record including
permissible maxima and minima for each parameter and filters
input values accordingly. Usually there are several possible
outputs (e.g., N vs T graphs and phase planes) which can also be
selected from the parameter input screen; alternatively, students
view the different outputs in sequence, by pressing the space bar
between views. Context-sensitive help screens are available
(press <F1>) from the input and output screens of every model,
and by pressing <F1> twice one can see a menu of additional help
screens that include discussions of function and editing key
assignments implemented by the program, printing protocols, video
options, etc.
Hardware Requirements
Populus is written in Borland Pascal 7.0 to run under DOS on IBM
and compatible computers. The program is offered in a
protected-mode version for computers with 286, 386, 486, or
pentium microprocessors and 2 MB RAM. There is also a real-mode
version for XT class computers with the 8088 chip. Full
implementation of Populus in real mode requires about 500KB of
RAM, free of memory-resident utilities and drivers. The
real-mode program will use LIM expanded memory, reducing the
frequency of disk reads and speeding program execution. Although
the code will emulate an xx87 coprocessor if one is not present,
many of the models are computationally intensive and will run
much more rapidly on a machine with the floating-point chip.
Version 3.4 will run on any IBM-compatible video system
that permits graphic displays, including "Hercules," "CGA,"
"EGA," "VGA," and "IBM8514." There are also VESA drivers for
800x600, 1024x768, and 1280x1024 pixels. In most cases, the
software will recognize and accommodate your video system
automatically. If your display emulates one of the color systems
in shades of gray (as many LCD screens do, with varying success),
consider using the option which forces output to the monochrome
mode. The IBM8514 system is detected as VGA by Turbo Pascal;
IBM8514 users who desire full 1024x768 resolution can select that
video mode from the Populus Options Menu (Alt-O) and save a
populus.cfg file to disk so that their preferred configuration
loads automatically each time the program is run.
Populus 3.4 contains a set of commercially produced drivers
by Ryle Design that supports a wide variety of printers,
including 9-pin and 24-pin dot matrix printers, HP laserjets and
deskjets, the HP paintjet, and printers implementing the
Postscript page-description language. Print files may also be
saved to disk and sent to the printer later using the DOS Print
command. Set the appropriate printing configuration on the
Populus options menu. Note that Postscript supports
graphics-mode printing only. Our introductory narratives and all
outputs are rendered in graphics mode, but the parameter inputs
and help windows are text mode screens. To print them on a
postscript laser printer you will have to set it up as an HP
emulator.
Bells and Whistles
For many problems and exercises it is desirable that
students be able to read numerical values accurately from the
graphical output. We have included several new video routines
for this purpose. A gridding function (press <Alt-G>) plots
horizontal and vertical lines from the major axis ticks, and a
second <Alt-G> grids the minor ticks. A third press toggles the
feature off. Our video zooming function (press <Alt-Z>) pops up
a rectangle whose corners can be moved (with the cursor keys) to
any point on screen. Pressing <Enter> then zooms this new
rectangle to full-screen size. By zooming in on an interesting
equilibrium region and gridding the output, final frequencies can
be read with any desired degree of accuracy.
For many time trajectories of ecological dynamics,
comparison of arithmetic and logarithmic plots has pedagogical
value. Populus plots arithmetic time trajectories by default but
allows you to toggle a semi- logarithmic plot (press <Alt-L>).
Like other video utilities in Populus, the feature is turned off
(and the screen-bottom options line is cleared) with the same
<Alt-L> keystrokes that turned it on.
Populus models that display <F4> in the lower-right corner
of their input window include a routine that allows on-screen
comparison of outputs resulting from two different sets of
parameter values. To implement this feature, simply toggle <F4>.
Graphical output from the current parameter values will be
plotted in the normal colors, while output of the previous run
will be shadowed in black. A second press of <F4> toggles the
graphical comparison routine off.
Stability analyses are important in helping students to
understand the dynamics of ecological and evolutionary models,
and we have provided a rich set of stability tools in Populus.
Many of the genetical simulations begin from several different
starting gene frequencies automatically. Optional stability
analyses are also available with the phase-plane graphs of
ecological dynamics. To implement this feature, press <Alt-S>
after a phase diagram is complete; a cursor will pop up and can
be moved to any point on the screen. Pressing <Enter> will then
initiate a trajectory from that point, and the dynamics can be
run forward or backward. Alternatively, multiple-starting-point
stability analyses may be run by pressing <m> after <Alt-S>. The
program will then initiate trajectories from the perimeter or
from a gridded pattern of points (the number and position of
starting points is set from the options menu) to illustrate the
stability of internal equilibria.
In addition to these video utilities, Populus now includes
several file- handling routines. Output data from any of the
simulations can be saved to disk for analysis using a
spreadsheet, statistical package, or graphics editor. To do so,
call up the options menu after running your simulation, and
specify a path and name for your data file. Similarly, Populus
can save to disk and reload sets of model parameter values; you
might use this feature to save a series of parameter files that
show particularly instructive examples, and ask your students to
load, run, and analyze them as part of a lab exercise.
Finding Documentation
This file contains only a brief introduction to Populus.
Full descriptions of each feature and a listing of the keystrokes
necessary to call and implement it are built into the program,
and are accessible from the Main Help Menu. To see this menu,
press <F1> (or if you are already in one of the model parameter
or output screens, press <F1> twice, to get past the
context-sensitive help). We recommend a tour of the Main Help
Menu as the quickest way to familiarize yourself with the
capabilities of Populus.
Sponsorship and Distribution
This software is underwritten by the Undergraduate Course
and Curriculum Development Program of the National Science
Foundation (USE-9150887, USE-919155967, DUE-9354777); it is not a
commercial venture and we encourage you to distribute it without
charge to any colleague or student who will put it to good use.
If you find a bug please tell us. We will fix it and provide you
with an update.
Don Alstad Department of Ecology,
Evolution & Behavior University of Minnesota
1987 Upper Buford Circle St. Paul, MN
55108-6097 612-624-6748
[log in to unmask]
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There are now two versions of Populus posted on the
Minnesota Ecology Server (ecology.ecology.umn.edu, IP
134.84.144.16). A protected-mode version for 286 and later
microprocessors with 2MB RAM is compressed in the file
pop34P.exe. A real-mode version for older XT-class computers is
compressed in the file pop34R.exe.
In addition to this read.me, the protected mode version
contains five files as follows:
1) Populus.doc is an ascii text file that explains features and
requirements of the software. We suggest that you read it before
using the program. Note that full documentation is an internal
part of Populus, accessible from the main help menu (press <F1>
once, or twice depending on context), and that many program
features are adjusted from the Options Menu (press <Alt-O>).
2) Populus.exe is the binary executable file that runs the
protected-mode version; it should be placed in the hard-drive
directory that you will use when running Populus.
3) Populus.txt contains all of the text screens that are
displayed by Populus. Populus.txt is indexed for rapid retrieval
to screen, and is not an ascii file; you will not be able to
simply dump it to a printer. If you would like to print an
introductory narrative, do so from within the populus program. I
will make expanded versions of these narratives (with
illustrating graphics and suggested exercises) available in a
book.
4) DBMI16BI.ovl is a DOS Protected Mode Interface Server that is
required for Populus to run in the protected mode. We are
licensed by Borland Internation- al to distribute it with our
program.
5) RTM.exe is a run-time manager that loads Populus in the
protected mode and provides a protected mode memory manager. It
is also a Borland product. All six of these files should be
housed together in the same directory, or linked by a path
command. To run the protected-mode Populus, type "populus"
<enter>.
The real-mode version of Populus includes four files in
addition to this read.me, as follows:
1) Populus.doc serves both Populus versions and is described
above.
2) Populusr.exe is the binary executable file that runs the
real-mode version; it should be placed in the hard-drive
directory that you will use when running Populus. Note the extra
letter r in the file name, for "real-mode."
3) Populusr.ovr contains the overlays that swap different models
and routines in and out of computer memory. This file is
required to run the program.
4) Populus.txt is used by both versions of Populus, and is
described above. All six of these files should be housed
together in the same directory, or linked by a DOS path command.
To run the protected-mode Populus, type "populusr" <enter>.
Populus allows you to save other files to disk. For
example, if you elect to preserve any of the configuration
information chosen from the Populus options menu, the program
will save a populus.cfg file and your configuration will be
loaded automatically each time Populus starts. Parameter sets,
print files, and data outputs may also be saved with filenames
(*.par, *.prn and *.dat) of your choosing, but only the files
listed above are necessary to run the program.
We encourage you to give this software without charge to any
students or colleagues who will put it to good use. When you do
so, please pass on the entire protected- or real-mode package
intact. File sizes should be as follows:
populus.doc 8347 bytes populus.exe 1070080
bytes populus.txt 838959 bytes read.me 4578
bytes DPMI16BI.ovl 65376 bytes RTM.exe 108846
bytes populusr.exe 110624 bytes populusr.ovr
878107 bytes
If the file sizes that you receive differ from these values, your
copy is corrupt and should be destroyed.
We will maintain current copies of Populus in the
/pub/populus subdirec- tory of ecology.ecology.umn.edu for
anonymous FTP. Users who leave an email address as requested
will be notified when a new version of the program is posted. If
you lack the facilities to acquire Populus over the internet, we
will provide you with a disk by snail mail for $10 payable to the
University of Minnesota. Write to Don Alstad, Department of
Ecology, Evolution and Behavior, University of Minnesota, 1987
Upper Buford Circle, St. Paul, MN 55108-6097. Please do not
send purchase orders.
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Ferson,Scott; H. Resit Akcakaya (1991): RAMAS / AGE. (Applied
Biomathematics 100 North Country Road Setauket, NY 11733)
[ECOLOGY, MODELING, POPULATION, SINGLE POPULATION, DOS<The
software serves a very specific purpose. The purpose of the
program is to model a single population based on various factors
that affect the population's growth and development. If this is
the sole purpose of the user then the software would come in
handy, and the graphs would prove helpful in demonstrating the
relationship between various factors and each age group. If
someone had a lot of information about a single species, the
software would be useful in relating the information. The
problems I had with the program are it could not be used easily
without a manual, it is not very practical to use to simulate
arbitrary situations, and it is not very informative. In my
opinion the program would only prove to be useful if the user has
knowledge of age-structured population dynamics and wants to
relate information on a specific example. For another review
refer to SCIENTIFIC SOFTWARE winter 1991-1992 page 5.>
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