Bio Education Software FAQ (3 of 3)

Eli Meir meir at zoology.washington.edu
Thu Sep 21 18:24:38 EST 1995


(5)  Cell and Molecular Biology

(5a)	Genetics Construction Kit

This is a problem-solving program based on fly genetics.  You get a
vial of flies, with 
certain traits, and you have to figure out the genetics of those traits
by doing various 
crosses.  The traits can range from simple dominant/recessive to
multiple gene, multiple 
allele systems with codominance, linkage, sex-linkage, and probably
more.  The flies 
come in vials, which are each shown as separate windows on the screen. 
To start out you 
can pick flies with known mutations, or you can ask the program to
randomly create 
mutant flies.  To cross two flies you simply click on each of them
(making sure one is 
male and the other is female), and then select cross from the menu.  A
new window 
appears showing the results of the cross.  You can also look at tables 
of the results of 
crosses, do chi-square analysis, and make notes in a simple
word-processor window.  As 
a note of historical interest, I believe that this is the original
BioQuest program.

The program has a nice intuitive interface, making it easy to conduct
the crosses and look 
at the results.  Unfortunetly, the program was designed to be run on
old macintoshes with 
small, black and white screens, so everything on the screen is small
and there is no color.  
All flies look the same, no matter what their mutations.  Despite this
small caveat, this 
program is really well done and engaging.  My hunch is that using this
program, students 
will gain a greater understanding of why they make different crosses
and what the results 
mean than they would with a wet lab, because they wonÕt have to worry
about taking care 
of the real flies and everything happens in a few minutes instead of a
few weeks.  Thus I 
would guess that this program should be good for either replacing or
supplementing a 
typical introductory fly genetics laboratory.

Computer:  Macintosh

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

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



(5b)	Virtual Fly Lab

This world wide web site lets you do fly breeding experiments very
similar to those 
which students do in introductory genetics courses.  The flies in this
simulation have nine 
traits (e.g. bristle type, eye color, wing shape) each with multiple
possible phenotypes 
including Òwild typeÓ.  For each trait, you can get a picture of each
phenotype.  You start 
by specifying the traits of the two parent flies, which you then mate. 
The results of this 
mating are shown to you as a list of the traits of each type of
offspring, as well as a table 
showing what proportion of the female and male offspring had each
trait.  These 
proportions are not perfect genetic proportions like 50/50, but include
some error.  If you 
want to, you can also get pictures of what each type of offspring fly
looks like.  These 
pictures are useful in some cases (eye color), and not so useful in
others where the trait is 
not easily visible in a picture of a whole fly (bristle type).  You can
then select a male and 
female from the offspring to do a further cross or backcross to one of
the parents.  You 
can also do a chi-square analysis of the results from your cross. 

While the web site is labelled ÒWarning:  ExperimentalÓ it seems to
work quite nicely for 
me.  Getting the results of your crosses over the web can sometimes be
a bit slow, even 
with a high-speed connection, but its not too slow to be unbearable
(and certainly much 
faster than real life, plus you donÕt have to be constantly on the
lookout for virgin 
females).  For anyone who is comfortable using a web browser, the
interface is quite easy 
to use, and being able to get pictures of each fly brings the
simulation to life a little more 
than other fly genetics programs.  One drawback to the program is that
you canÕt look at 
results of more than one cross side by side - everything is done on
separate pages because 
of the way the world wide web works, and you must flip back and forth
between pages to 
make comparisons.  You also canÕt cross the offspring of one experiment
with the 
offspring from another, or with a new type of fly which you make up. 
Still, this is a very 
nice program, and should be quite useful as a substitute or enhancement
of the traditional 
undergraduate fly genetics lab.

Computer:  World Wide Web

Source:  http://vflylab.calstatela.edu/edesktop/VirtApps/VflyLab/

Cost:  Free


(5c)	SequenceIt!

This program is a puzzle-solving program.  You are presented with a
completely 
unknown protein and asked to sequence it, using around two dozen
standard (I assume) 
biochemical techniques, such as acid and base degradation, cleavage by
various 
proteases, various degradation techniques, and so on.  Again, this
program has a very nice 
display and user-interface, with some cute (though probably eventually
annoying) 
animations.  I suspect students would have a lot more fun with it than
with the standard 
cookbook chem lab exercises, since you can concentrate on the puzzle
instead of the 
vials.

Computer:  Macintosh

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

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

(5d)	PurifyIt!

This program is another puzzle solving program similar in design to
SequenceIt! above, 
except here you get a flask with a number of proteins in it, and you
have to purify one of 
them, using one of a number of standard (I assume) purification
techniques such as 
dialysis and various gel schemes.  This program seems a little
unfinished, with not quite 
as good an interface as SequenceIt!, but basically they are the same
concept.

Computer:  Macintosh

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

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

(5e)	RateIt!

In this program you are given flasks of enzymes, substrates,
inhibitors, etc., and you must 
perform various tests to discover the kinetic properties of the
enzymatic system, using 
standard tools and experiments of enzymoligists (is that a real term). 
You can change 
pH, temperature, etc. and do experiments to find rates of enzyme
activity.  You can also 
compare results to theoretical models such as michaelis-menton.  (This
program only got 
a short look, so there may be a lot more here).

Computer:  Macintosh

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

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

(5f)	Enzyme

This is a combination of a hypercard stack with a simulation of enzyme
kinetics.  The 
hypercard stack provides the front-end which lets the user change
parameters in the 
model and determine reaction rates.  Has graphing capabilities for the
results.  Quite 
nicely done.  This program is not, however, as comprehensive as the
BioQuest version, 
and only includes two built-in enzymes (I do not see a way to add
more).

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

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

Cost:  Free

(5g)	MacMolecule

This program allows you to build and display models of molecules.  It
will do any of 
three traditional diplay type - ball and stick, space-filling, and
wire-frame.  The molecules 
are displayed really nicely, in full-color, and you can rotate them
around using the mouse 
(its fast! - quite impressive).  They have some molecules included, and
you can make 
your own with a word-processor.

Computer:  Macintosh

Source:  anonymous ftp sites

Cost:  Free


(5h)	Visual Genetics

(Note - we have only seen a demo version)
This is a series of animations designed to accompany a course in cell
and molecular 
biology.  The animations are divided into seven categories: DNA
structure and 
replication, Protein synthesis, Cell division, Recombination and
mapping, Mutation repair 
and regulation, Biotechnology techniques, and Cell biology.  Each
category has 
approximately 10 animations in it.  The animations are more than
stick-figure but less 
than realistic-looking, and are stopped many times to show explanatory
text and labels.  
Along with animations, the program has multiple choice and
problem-solving questions, 
and can also present you with a diagram which you must then label
correctly.  You can 
input your own questions if you wish.  None of these were active in the
demo version.

In the demo version we saw, only two animations are active, a
demonstration of meiosis, 
and an animation of several biochemical techniques for separating out
proteins, dna, and 
rna.  The meiosis animation seems useful to me as a visual aid in
understanding what is 
happening, since meiosis is a confusing concept for many students, and
the animation can 
show the steps fairly clearly.  The biochemical techniques animation
seems less useful, 
and I believe a good description in a textbook with nice pictures
should do just as well or 
better at explaining the techniques.  However, perhaps the television
appeal of having 
things move on the screen will help some students to remember these
techniques better 
than they would have through reading.  In general, this package should
help students who 
learn visually to understand and remember some introductory concepts in
cell and 
molecular biology, as an adjunct to (but not a replacement for) a good
textbook, 
laboratory, and video tapes of live cells.  It should be especially
helpful for things such as 
meiosis and dna replication which are somewhat complicated to visualize
from a 
description in a textbook.

Computer:  Macintosh and IBM

Source:  BioAnimate Productions, 28 Askin St., London, Ont. N6C 1I3. 
Phone: 	
	519-432-5800.  email: aday at julian.uwo.ca.  Demo available from 	
	http://www.inform.umd.edu/EdRes/Topic/AgrEnv/Biotech/Software/bio-	
	anim

Cost:  Low to High (depending on number of animations purchased)

(5i)	Virtual Genetics Laboratory

(Note - we have only seen a demo version).
This program takes the user through a series of genetics experiments
with fungi.  In the 
first experiment, you isolate 3 strains of fungi which are mutant for
an amino acid 
synthesis enzyme, and conduct plating experiments to determine which
amino acid they 
require.  The next experiment is to take 10 mutants for synthesis of
arginine, and try to 
figure out what step in the synthesis process each one is mutant for by
growing them on 
media with intermediates in the synthesis.  Then you do a similar
exercise using 
complementation tests.  The last three exercises are to do a
three-point cross, a tetrad 
analysis, and to use mitotic recombination to map genes.  Each
experiment is presented in 
a single screen, and you use the mouse to drag the items you will need
for each 
experiment to the appropriate places (ie - drag a mutant to the petri
dish, then drag 
different amino acids to the corners of the dish).  Results are
summarized for you in an 
onscreen table, and from these results you must draw appropriate
conclusions, which the 
program will tell you if you got right or not.  For each experiment,
the program provides 
a few paragraphs of background at the beginning, on-screen
instructions, and for some 
experiments it also provides one or more animations giving more
background on the 
technique (only one animation is active in the demo).

The program is laid out very well.  The main screen used for each
experiment is easy to 
understand and attractive, and the actions you need to perform are
simple, with the results 
shown clearly on the same screen.  The instructions give the right
amount of guidance 
and most students should be able to go through all the exercises with
minimal help from 
an instructor.  The animations (really more like highly abbreviated
textbook chapters with 
blinking pictures) add good background information and are also quite
clear, though 
controlling their speed takes a bit of getting used to.  This program
could be used as an 
adjunct or possibly a replacement for a fungal genetics lab, to let
students try out these 
techniques and practice interpreting the results in much less time and
without the 
technical difficulties of doing it for real.  The one drawback to this
program is that unlike 
some other simulated experiment programs mentioned in this FAQ, the
results are the 
same each time, and the student is not really carrying an experiment
through from an 
unknown start to a conclusion.  Still, this program should be very good
for teaching 
students some basic genetics techniques in a two to three hour lab.

Computer:  IBM (Windows 3.1 )

Source:  BioAnimate Productions, 28 Askin St., London, Ont. N6C 1I3. 
Phone: 	
	519-432-5800.  email: aday at julian.uwo.ca.  Demo available from 	
	http://www.inform.umd.edu/EdRes/Topic/AgrEnv/Biotech/Software/bio-	
	anim

Cost:	High


(5j)	Photosynthesis Multimedia Textbook

(Note - we have only seen a demo version)
This program takes the student through the process of photosynthesis,
using pictures of 
plants and animations of molecules to explain the different steps in
the process.  The 
animations look like standard textbook pictures of the various proteins
involved 
embedded in membranes or floating around in space, with little colored
balls bouncing 
around between the proteins representing the atoms and electrons that
are being 
manipulated by the proteins.  Each step in photosynthesis has its own
animation, and 
these are connected through a larger scale animation which shows the
whole process on 
one screen.  The demo version includes only the pictures, without any
text, but the real 
version also has a sidebar with text explaining each step.  You
progress through the 
material using a VCR like control bar at the bottom of the screen which
is quite easy to 
use, or you can skip around to different sections from the menus.  The
whole thing takes 
around 15 or 20 minutes to skim through, though to go through it
thoroughly probably 
takes considerably longer.

The animations are crisp and nicely done, with graphics that are simple
enough to be able 
to follow but spiffy enough to look professional.  The user interface
should be trivial for 
most students to learn.  Assuming that the text accompanying the
graphics gives good 
descriptions of whatÕs going on (its missing in the demo), this program
may make a nice 
companion to a textbook description of photosynthesis, or individual
animations could be 
used in a classroom to visually demonstrate whatÕs happening instead of
just talking 
about it.  If your students have trouble following the reactions in
photosynthesis and you 
think that simple animations might help them, then this program should
be useful for you.

Computer:  Macintosh

Source:  John M. Cheeseman or Matej Lexa, Dept of Plant Biology, Univ
of Illinois, 
Urbana, IL 61801.  Email m-lexa at uiuc.edu.  Demo version and info
available from 
http://www.life.uiuc.edu/cheeseman/home.html

Cost:	Low


(6)	General purpose software useful in education

(6a)	Stella   [EM and AS]

This program lets you construct and run mathematical models using a
very easy to 
understand graphical interface.  For each element in your model, you
make a box on the 
screen.  Inside that box, you put the starting amount of that element. 
Then you use the 
mouse to draw arrows between the boxes representing flows of stuff from
one box to 
another, or effects of one box on another.  For each arrow, you type in
an ordinary 
differential equation which specifies what that arrow does.  For
instance, to model growth 
of a tree, you might have a tree box, a sunlight box and a CO2 box, and
arrows coming 
from the sunlight and the CO2 into the tree.  The tree would start out
with a certain mass, 
and the sunlight and CO2 could each be given appropriate starting
values and changes 
over time (e.g. you could put the sun on a 24 hour cycle by modelling
it with a sine wave) 
and you would have some equation like dTree/dt = function(sunlight,
CO2) associated 
with the arrows.  Then you could run this model and watch the tree
grow.  The growth of 
the tree would be represented both by the tree box filling up, and you
can also make 
graphs of any of the variables over time.

This program is really nicely designed for teaching.  The learning
curve is quite small, 
and even though the equations are not hidden from the user, the
interface makes the 
mathematics behind the models quite transparent.  Yet the mathematics
is still rigorous, 
and once students learn to use this tool they can use it for high
quality work (plenty of 
researches use Stella as well).  Instructors could also use this
program to set up models 
ahead of time which the students could then play with, though if one of
the other 
programs mentioned in this FAQ does that model, its probably better to
use the special 
program.  I think Stella should be useful from advanced undergraduate
level courses 
where modelling is discussed all the way through graduate level
courses.  One warning is 
that (as with any mathematical programs) the instructor should probably
know something 
about numerical solution techniques if you do not want to get into
trouble.

Computer:  Macintosh (and IBM ?).

Source:  High Performance Software

Cost:  Low (ask for educational pricing)


(6b)	Extend

We have not seen this program, except as part of other teaching
programs mentioned in 
this FAQ (NeuroLab, Environmental Decision Making).  It appears to be a
Stella-like 
modelling program, with cuter graphics and a more flexible interface.

Computer:  Macintosh (and IBM?)

Source:

Cost:  High?

(6c)	Mathematica  [EM and AS]

Mathematica is a symbolic equation solver.  This means that you can
type in something 
like Integrate 2x + 5 and it will spit back x^2 + 5x + C.  This is only
the simplest example 
of what it can do.  You can give much more complicated equations and
ask it to integrate, 
differentiate, find roots, and many other mathematical operations.  All
functions can be 
plotted in many ways, and there are lots of other useful things
included (fourier 
transforms, etc.).

This program has a pretty large learning curve, but once you get over
the top of the curve 
it is a very powerful tool for doing all kinds of modelling.  As such,
it should be quite 
useful in an advanced undergraduate course or in graduate courses with
an emphasis  on 
modelling biology.  For more introductory level courses, the program
could probably be 
used by an instructor to make a model which students could then play
with.  However, if 
one of the other programs described in this FAQ includes the desired
model then you 
should probably use the specialized program.

Computer:  Macintosh, IBM, UNIX

Source:  Available commercially through software stores and mail-order.

Cost:  High


(6d)	Maple  [EM and AS]

Maple is a symbolic equation solver.  See the description of
Mathematica above.

Maple has the advantage over Mathematica of being faster, and having
better solvers.

Computer:  Macintosh, IBM, UNIX

Source:  Available commercially through software stores and mail-order.

Cost:  High

(6e)	Matlab

(6f)	LabView  [EM and DB]

LabVIEW is a very powerful data acquisition and analysis program. While
the program is 
not made specifically for education, many people use it in physiology
laboratories to 
make data collection easy for the students. Essentially LabVIEW is a
graphical 
programming environment that uses the construction of virtual
instruments as a 
metaphor. The front panel (the user interface) consists of various
controls and indicators 
(such as graphs, buttons, knobs, etc) and is built graphically by
placing different 
components in a window, and using the mouse to move them around and
resize them just 
the way you want them. The diagram (the code that determines the
instruments behavior) 
is also built graphically by wiring together icons that represent
various functions into a 
flowchart. Traditional programming structures such as loops and cases
are available. A 
high  degree of modularity is supported due to the ability of one
instrument to  access 
another as an icon within the diagram. LabVIEW ships with a large
library of routines for 
data analysis (FFTs, statistics, etc.). 

As is apparent from the above description, LabVIEW does take a little
skill to use. While 
many pre-made instruments are available which do quite a few of the
things you are 
likely to want in a classroom, inevitably you will want to modify them.
This does not take 
a full-blown programmer, but there is a learning curve. On the plus
side, once you figure 
your way around LabVIEW, you will be able to make highly custom
programs for each 
lab in your course quite easily. Such programs could include complex
simulations in 
addition to traditional data acquisition. Also, there are many other
teachers using 
LabVIEW for classes, so you may be able to take modules developed by
others and use 
them as is.  All in all, if you are setting up a physiology lab where
you intend to use 
computers, then Labview is a very nice program to use for that. 

Computer:  Macintosh, Windows, Sun

Source:  National Instruments, 1-800-433-3488.

Cost:  High

(6g)	SuperScope    [EM and DB]
Superscope is a general purpose data collection and analysis program,
similar to LabView 
(described above). It is a very powerful research tool, but is also
used in teaching. From 
within SuperScope, you can design programs that will collect and
process data in many 
different ways.  While the design process is not as graphical as in
LabVIEW, the basic 
idea and functionality is the same. SuperScope is more tightly focused
on data acquisition 
and is quicker to get up and running, but less customizable.  Elements
of the user 
interface (graphs, buttons, etc.) can be positioned in a window and
assigned tasks written 
in a macro language. However, SuperScope is not a programming
environment (for better 
or worse, you pick). SuperScopes macro language does include a library
of data analysis 
routines. 

(We have not used Superscope extensively, and so are not providing a
review).

Computer:  Macintosh

Source:  GW Instruments, 617-625-4096.

Cost:  High


(6h)	Spike Studio

Spike Studio is a data acquisition and analysis program written for
researchers in 
neurophysiology, and is also used in several neurophysiology laboratory
courses.   It was 
written by the author of this FAQ, so take this description and review
with a grain of salt.  
The program will collect data from several brands of digitizing board
(including the 
macintosh built-in microphone), will show the data on the screen, and
includes several 
types of analyses including spike and burst discrimination, determining
frequencies, data 
averaging, and some other tools commonly used by neurophysiologists.

While Spike Studio is not flexible in the way that LabView and
SuperScope are, it will do 
many of the things you would want in a teaching program.  Its two
advantages are that it 
does not require any programming or much set-up on your part, and more
importantly its 
free.

Computer:  Macintosh

Source:  anonymous ftp sites, such as info_mac or umich.

Cost:  Free




(7)	Textbooks on CD


(8)	Mosaic Sites and other random stuff

(8a)	Institute for Molecular Virology 

This site has lots of very pretty pictures of x-ray reconstructions of
viral structures.  It 
also has a few animations of things like a virus binding to its host,
and interactive pictures 
where you can rotate viral structures around.  In addition, this site
is a good source of 
other information on viruses and virologists.

URL: http://www.bocklabs.wisc.edu/


(8b)	BioCatalog

This is a collection of descriptions of software useful for biologists.
 They describe a few 
dozen packages, both commercial and public domain, with information on
how to get 
ahold of them, but no reviews.  Almost all the programs are for
molecular biologists, 
falling into categories such as DNA, Proteins, Molecular Evolution, and
so on.

FTP:  ftp.ebi.ac.uk     Directory: /pub/databases/bio_catal
URL:  http://www.ebi.ac.uk/biocat/biocat.html

(8c)	Neurosciences on the Internet

This site has a ton of cross-links to different places on the internet
with interesting 
neuroscience content.  Included are links to some programs mentioned in
this FAQ.

URL:  http://www.lm.com/~nab/

(8d)	Quantitative Training for Life Sciences

This site contains a number of public domain programs for biology
instruction, as well as 
links to other sites with more programs or demos.  This site also
contains a number of 
reviews of biology education software done by undergraduates at the
University of 
Tennessee, in a format similar to the reviews in this FAQ.

URL:  http://archives.math.utk.edu/mathbio/
ftp/gopher address:   archives.math.utk.edu

(9)  Acknowledments

Eli Meir is a Howard Hughes Medical Institute Predoctoral Fellow
(obligatory 
acknowledgement).


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




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