(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
program has a nice intuitive interface. As a note of historical
interest, I believe that this is the original BioQuest program.
Computer: Macintosh
Source: BioQuest asdg at umdd.umd.edu or see address above under
Resources.
Cost: Low (single user) / High (site license)
(5b) 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)
(5c) 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 theyÕre
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)
(5d) 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)
(5e) 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 donÕt see a way to add more).
Computer: Macintosh, also needs Hypercard 2.2 (wonÕt work with
Hypercard player).
Source: David Kesler, Rhodes College. email: KESLER at ns.rhodes.edu
Cost: Free
(5f) 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
(5g) 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- an
im
Cost: Low to High (depending on number of animations purchased)
(5h) 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 youÕll 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- an
im
Cost: High
(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 ÔtreeÕ box, a
ÔsunlightÕ box and a ÔCO2Õ 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 ÔdTree/dt = function(sunlight, CO2)Õ 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 donÕt want to get into trouble.
Computer: Macintosh and IBM.
Source: High Performance Software. See web site at
http://www.valley.net/~hps/stella.html
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 ÔIntegrate 2x + 5Õ and it will spit back Ôx^2 +
5x + CÕ. 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 instrument's 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 isn't a programming environment
(for better or worse, you pick). SuperScope's 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. ItÕs 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://mathsun1.math.utk.edu:8000/~gross/quant.lifesci.html
ftp/gopher address: archives.math.utk.edu
(9) Acknowledments
Eli Meir is a Howard Hughes Medical Institute Predoctoral Fellow
(obligatory acknowledgement).
